Merge origin/main into feat/kotlin-language-support

.claude/skills/gitnexus/gitnexus-cli/SKILL.md

@@ -0,0 +1,82 @@
+---
+name: gitnexus-cli
+description: "Use when the user needs to run GitNexus CLI commands like analyze/index a repo, check status, clean the index, generate a wiki, or list indexed repos. Examples: \"Index this repo\", \"Reanalyze the codebase\", \"Generate a wiki\""
+---
+
+# GitNexus CLI Commands
+
+All commands work via `npx` — no global install required.
+
+## Commands
+
+### analyze — Build or refresh the index
+
+```bash
+npx gitnexus analyze
+```
+
+Run from the project root. This parses all source files, builds the knowledge graph, writes it to `.gitnexus/`, and generates CLAUDE.md / AGENTS.md context files.
+
+| Flag           | Effect                                                           |
+| -------------- | ---------------------------------------------------------------- |
+| `--force`      | Force full re-index even if up to date                           |
+| `--embeddings` | Enable embedding generation for semantic search (off by default) |
+
+**When to run:** First time in a project, after major code changes, or when `gitnexus://repo/{name}/context` reports the index is stale.
+
+### status — Check index freshness
+
+```bash
+npx gitnexus status
+```
+
+Shows whether the current repo has a GitNexus index, when it was last updated, and symbol/relationship counts. Use this to check if re-indexing is needed.
+
+### clean — Delete the index
+
+```bash
+npx gitnexus clean
+```
+
+Deletes the `.gitnexus/` directory and unregisters the repo from the global registry. Use before re-indexing if the index is corrupt or after removing GitNexus from a project.
+
+| Flag      | Effect                                            |
+| --------- | ------------------------------------------------- |
+| `--force` | Skip confirmation prompt                          |
+| `--all`   | Clean all indexed repos, not just the current one |
+
+### wiki — Generate documentation from the graph
+
+```bash
+npx gitnexus wiki
+```
+
+Generates repository documentation from the knowledge graph using an LLM. Requires an API key (saved to `~/.gitnexus/config.json` on first use).
+
+| Flag                | Effect                                    |
+| ------------------- | ----------------------------------------- |
+| `--force`           | Force full regeneration                   |
+| `--model <model>`   | LLM model (default: minimax/minimax-m2.5) |
+| `--base-url <url>`  | LLM API base URL                          |
+| `--api-key <key>`   | LLM API key                               |
+| `--concurrency <n>` | Parallel LLM calls (default: 3)           |
+| `--gist`            | Publish wiki as a public GitHub Gist      |
+
+### list — Show all indexed repos
+
+```bash
+npx gitnexus list
+```
+
+Lists all repositories registered in `~/.gitnexus/registry.json`. The MCP `list_repos` tool provides the same information.
+
+## After Indexing
+
+1. **Read `gitnexus://repo/{name}/context`** to verify the index loaded
+2. Use the other GitNexus skills (`exploring`, `debugging`, `impact-analysis`, `refactoring`) for your task
+
+## Troubleshooting
+
+- **"Not inside a git repository"**: Run from a directory inside a git repo
+- **Index is stale after re-analyzing**: Restart Claude Code to reload the MCP server
+- **Embeddings slow**: Omit `--embeddings` (it's off by default) or set `OPENAI_API_KEY` for faster API-based embedding

.claude/skills/gitnexus/gitnexus-debugging/SKILL.md

@@ -6,6 +6,7 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 # Debugging with GitNexus
 
 ## When to Use
+
 - "Why is this function failing?"
 - "Trace where this error comes from"
 - "Who calls this method?"
@@ -37,17 +38,18 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 
 ## Debugging Patterns
 
-| Symptom | GitNexus Approach |
+| Symptom              | GitNexus Approach                                          |
-|---------|-------------------|
+| -------------------- | ---------------------------------------------------------- |
-| Error message | `gitnexus_query` for error text → `context` on throw sites |
+| Error message        | `gitnexus_query` for error text → `context` on throw sites |
-| Wrong return value | `context` on the function → trace callees for data flow |
+| Wrong return value   | `context` on the function → trace callees for data flow    |
-| Intermittent failure | `context` → look for external calls, async deps |
+| Intermittent failure | `context` → look for external calls, async deps            |
-| Performance issue | `context` → find symbols with many callers (hot paths) |
+| Performance issue    | `context` → find symbols with many callers (hot paths)     |
-| Recent regression | `detect_changes` to see what your changes affect |
+| Recent regression    | `detect_changes` to see what your changes affect           |
 
 ## Tools
 
 **gitnexus_query** — find code related to error:
+
 ```
 gitnexus_query({query: "payment validation error"})
 → Processes: CheckoutFlow, ErrorHandling
@@ -55,6 +57,7 @@ gitnexus_query({query: "payment validation error"})
 ```
 
 **gitnexus_context** — full context for a suspect:
+
 ```
 gitnexus_context({name: "validatePayment"})
 → Incoming calls: processCheckout, webhookHandler
@@ -63,6 +66,7 @@ gitnexus_context({name: "validatePayment"})
 ```
 
 **gitnexus_cypher** — custom call chain traces:
+
 ```cypher
 MATCH path = (a)-[:CodeRelation {type: 'CALLS'}*1..2]->(b:Function {name: "validatePayment"})
 RETURN [n IN nodes(path) | n.name] AS chain

.claude/skills/gitnexus/gitnexus-exploring/SKILL.md

@@ -6,6 +6,7 @@ description: "Use when the user asks how code works, wants to understand archite
 # Exploring Codebases with GitNexus
 
 ## When to Use
+
 - "How does authentication work?"
 - "What's the project structure?"
 - "Show me the main components"
@@ -37,16 +38,17 @@ description: "Use when the user asks how code works, wants to understand archite
 
 ## Resources
 
-| Resource | What you get |
+| Resource                                | What you get                                            |
-|----------|-------------|
+| --------------------------------------- | ------------------------------------------------------- |
-| `gitnexus://repo/{name}/context` | Stats, staleness warning (~150 tokens) |
+| `gitnexus://repo/{name}/context`        | Stats, staleness warning (~150 tokens)                  |
-| `gitnexus://repo/{name}/clusters` | All functional areas with cohesion scores (~300 tokens) |
+| `gitnexus://repo/{name}/clusters`       | All functional areas with cohesion scores (~300 tokens) |
-| `gitnexus://repo/{name}/cluster/{name}` | Area members with file paths (~500 tokens) |
+| `gitnexus://repo/{name}/cluster/{name}` | Area members with file paths (~500 tokens)              |
-| `gitnexus://repo/{name}/process/{name}` | Step-by-step execution trace (~200 tokens) |
+| `gitnexus://repo/{name}/process/{name}` | Step-by-step execution trace (~200 tokens)              |
 
 ## Tools
 
 **gitnexus_query** — find execution flows related to a concept:
+
 ```
 gitnexus_query({query: "payment processing"})
 → Processes: CheckoutFlow, RefundFlow, WebhookHandler
@@ -54,6 +56,7 @@ gitnexus_query({query: "payment processing"})
 ```
 
 **gitnexus_context** — 360-degree view of a symbol:
+
 ```
 gitnexus_context({name: "validateUser"})
 → Incoming calls: loginHandler, apiMiddleware

.claude/skills/gitnexus/gitnexus-guide/SKILL.md

@@ -0,0 +1,64 @@
+---
+name: gitnexus-guide
+description: "Use when the user asks about GitNexus itself — available tools, how to query the knowledge graph, MCP resources, graph schema, or workflow reference. Examples: \"What GitNexus tools are available?\", \"How do I use GitNexus?\""
+---
+
+# GitNexus Guide
+
+Quick reference for all GitNexus MCP tools, resources, and the knowledge graph schema.
+
+## Always Start Here
+
+For any task involving code understanding, debugging, impact analysis, or refactoring:
+
+1. **Read `gitnexus://repo/{name}/context`** — codebase overview + check index freshness
+2. **Match your task to a skill below** and **read that skill file**
+3. **Follow the skill's workflow and checklist**
+
+> If step 1 warns the index is stale, run `npx gitnexus analyze` in the terminal first.
+
+## Skills
+
+| Task                                         | Skill to read       |
+| -------------------------------------------- | ------------------- |
+| Understand architecture / "How does X work?" | `gitnexus-exploring`         |
+| Blast radius / "What breaks if I change X?"  | `gitnexus-impact-analysis`   |
+| Trace bugs / "Why is X failing?"             | `gitnexus-debugging`         |
+| Rename / extract / split / refactor          | `gitnexus-refactoring`       |
+| Tools, resources, schema reference           | `gitnexus-guide` (this file) |
+| Index, status, clean, wiki CLI commands      | `gitnexus-cli`               |
+
+## Tools Reference
+
+| Tool             | What it gives you                                                        |
+| ---------------- | ------------------------------------------------------------------------ |
+| `query`          | Process-grouped code intelligence — execution flows related to a concept |
+| `context`        | 360-degree symbol view — categorized refs, processes it participates in  |
+| `impact`         | Symbol blast radius — what breaks at depth 1/2/3 with confidence         |
+| `detect_changes` | Git-diff impact — what do your current changes affect                    |
+| `rename`         | Multi-file coordinated rename with confidence-tagged edits               |
+| `cypher`         | Raw graph queries (read `gitnexus://repo/{name}/schema` first)           |
+| `list_repos`     | Discover indexed repos                                                   |
+
+## Resources Reference
+
+Lightweight reads (~100-500 tokens) for navigation:
+
+| Resource                                       | Content                                   |
+| ---------------------------------------------- | ----------------------------------------- |
+| `gitnexus://repo/{name}/context`               | Stats, staleness check                    |
+| `gitnexus://repo/{name}/clusters`              | All functional areas with cohesion scores |
+| `gitnexus://repo/{name}/cluster/{clusterName}` | Area members                              |
+| `gitnexus://repo/{name}/processes`             | All execution flows                       |
+| `gitnexus://repo/{name}/process/{processName}` | Step-by-step trace                        |
+| `gitnexus://repo/{name}/schema`                | Graph schema for Cypher                   |
+
+## Graph Schema
+
+**Nodes:** File, Function, Class, Interface, Method, Community, Process
+**Edges (via CodeRelation.type):** CALLS, IMPORTS, EXTENDS, IMPLEMENTS, DEFINES, MEMBER_OF, STEP_IN_PROCESS
+
+```cypher
+MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "myFunc"})
+RETURN caller.name, caller.filePath
+```

.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md

@@ -6,6 +6,7 @@ description: "Use when the user wants to know what will break if they change som
 # Impact Analysis with GitNexus
 
 ## When to Use
+
 - "Is it safe to change this function?"
 - "What will break if I modify X?"
 - "Show me the blast radius"
@@ -37,24 +38,25 @@ description: "Use when the user wants to know what will break if they change som
 
 ## Understanding Output
 
-| Depth | Risk Level | Meaning |
+| Depth | Risk Level       | Meaning                  |
-|-------|-----------|---------|
+| ----- | ---------------- | ------------------------ |
-| d=1 | **WILL BREAK** | Direct callers/importers |
+| d=1   | **WILL BREAK**   | Direct callers/importers |
-| d=2 | LIKELY AFFECTED | Indirect dependencies |
+| d=2   | LIKELY AFFECTED  | Indirect dependencies    |
-| d=3 | MAY NEED TESTING | Transitive effects |
+| d=3   | MAY NEED TESTING | Transitive effects       |
 
 ## Risk Assessment
 
-| Affected | Risk |
+| Affected                       | Risk     |
-|----------|------|
+| ------------------------------ | -------- |
-| <5 symbols, few processes | LOW |
+| <5 symbols, few processes      | LOW      |
-| 5-15 symbols, 2-5 processes | MEDIUM |
+| 5-15 symbols, 2-5 processes    | MEDIUM   |
-| >15 symbols or many processes | HIGH |
+| >15 symbols or many processes  | HIGH     |
 | Critical path (auth, payments) | CRITICAL |
 
 ## Tools
 
 **gitnexus_impact** — the primary tool for symbol blast radius:
+
 ```
 gitnexus_impact({
   target: "validateUser",
@@ -72,6 +74,7 @@ gitnexus_impact({
 ```
 
 **gitnexus_detect_changes** — git-diff based impact analysis:
+
 ```
 gitnexus_detect_changes({scope: "staged"})
 

.claude/skills/gitnexus/gitnexus-pr-review/SKILL.md

@@ -0,0 +1,163 @@
+---
+name: gitnexus-pr-review
+description: "Use when the user wants to review a pull request, understand what a PR changes, assess risk of merging, or check for missing test coverage. Examples: \"Review this PR\", \"What does PR #42 change?\", \"Is this PR safe to merge?\""
+---
+
+# PR Review with GitNexus
+
+## When to Use
+
+- "Review this PR"
+- "What does PR #42 change?"
+- "Is this safe to merge?"
+- "What's the blast radius of this PR?"
+- "Are there missing tests for this PR?"
+- Reviewing someone else's code changes before merge
+
+## Workflow
+
+```
+1. gh pr diff <number>                                    → Get the raw diff
+2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
+3. For each changed symbol:
+   gitnexus_impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
+4. gitnexus_context({name: "<key symbol>"})               → Understand callers/callees
+5. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
+6. Summarize findings with risk assessment
+```
+
+> If "Index is stale" → run `npx gitnexus analyze` in terminal before reviewing.
+
+## Checklist
+
+```
+- [ ] Fetch PR diff (gh pr diff or git diff base...head)
+- [ ] gitnexus_detect_changes to map changes to affected execution flows
+- [ ] gitnexus_impact on each non-trivial changed symbol
+- [ ] Review d=1 items (WILL BREAK) — are callers updated?
+- [ ] gitnexus_context on key changed symbols to understand full picture
+- [ ] Check if affected processes have test coverage
+- [ ] Assess overall risk level
+- [ ] Write review summary with findings
+```
+
+## Review Dimensions
+
+| Dimension | How GitNexus Helps |
+| --- | --- |
+| **Correctness** | `context` shows callers — are they all compatible with the change? |
+| **Blast radius** | `impact` shows d=1/d=2/d=3 dependents — anything missed? |
+| **Completeness** | `detect_changes` shows all affected flows — are they all handled? |
+| **Test coverage** | `impact({includeTests: true})` shows which tests touch changed code |
+| **Breaking changes** | d=1 upstream items that aren't updated in the PR = potential breakage |
+
+## Risk Assessment
+
+| Signal | Risk |
+| --- | --- |
+| Changes touch <3 symbols, 0-1 processes | LOW |
+| Changes touch 3-10 symbols, 2-5 processes | MEDIUM |
+| Changes touch >10 symbols or many processes | HIGH |
+| Changes touch auth, payments, or data integrity code | CRITICAL |
+| d=1 callers exist outside the PR diff | Potential breakage — flag it |
+
+## Tools
+
+**gitnexus_detect_changes** — map PR diff to affected execution flows:
+
+```
+gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+
+→ Changed: 8 symbols in 4 files
+→ Affected processes: CheckoutFlow, RefundFlow, WebhookHandler
+→ Risk: MEDIUM
+```
+
+**gitnexus_impact** — blast radius per changed symbol:
+
+```
+gitnexus_impact({target: "validatePayment", direction: "upstream"})
+
+→ d=1 (WILL BREAK):
+  - processCheckout (src/checkout.ts:42) [CALLS, 100%]
+  - webhookHandler (src/webhooks.ts:15) [CALLS, 100%]
+
+→ d=2 (LIKELY AFFECTED):
+  - checkoutRouter (src/routes/checkout.ts:22) [CALLS, 95%]
+```
+
+**gitnexus_impact with tests** — check test coverage:
+
+```
+gitnexus_impact({target: "validatePayment", direction: "upstream", includeTests: true})
+
+→ Tests that cover this symbol:
+  - validatePayment.test.ts [direct]
+  - checkout.integration.test.ts [via processCheckout]
+```
+
+**gitnexus_context** — understand a changed symbol's role:
+
+```
+gitnexus_context({name: "validatePayment"})
+
+→ Incoming calls: processCheckout, webhookHandler
+→ Outgoing calls: verifyCard, fetchRates
+→ Processes: CheckoutFlow (step 3/7), RefundFlow (step 1/5)
+```
+
+## Example: "Review PR #42"
+
+```
+1. gh pr diff 42 > /tmp/pr42.diff
+   → 4 files changed: payments.ts, checkout.ts, types.ts, utils.ts
+
+2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+   → Changed symbols: validatePayment, PaymentInput, formatAmount
+   → Affected processes: CheckoutFlow, RefundFlow
+   → Risk: MEDIUM
+
+3. gitnexus_impact({target: "validatePayment", direction: "upstream"})
+   → d=1: processCheckout, webhookHandler (WILL BREAK)
+   → webhookHandler is NOT in the PR diff — potential breakage!
+
+4. gitnexus_impact({target: "PaymentInput", direction: "upstream"})
+   → d=1: validatePayment (in PR), createPayment (NOT in PR)
+   → createPayment uses the old PaymentInput shape — breaking change!
+
+5. gitnexus_context({name: "formatAmount"})
+   → Called by 12 functions — but change is backwards-compatible (added optional param)
+
+6. Review summary:
+   - MEDIUM risk — 3 changed symbols affect 2 execution flows
+   - BUG: webhookHandler calls validatePayment but isn't updated for new signature
+   - BUG: createPayment depends on PaymentInput type which changed
+   - OK: formatAmount change is backwards-compatible
+   - Tests: checkout.test.ts covers processCheckout path, but no webhook test
+```
+
+## Review Output Format
+
+Structure your review as:
+
+```markdown
+## PR Review: <title>
+
+**Risk: LOW / MEDIUM / HIGH / CRITICAL**
+
+### Changes Summary
+- <N> symbols changed across <M> files
+- <P> execution flows affected
+
+### Findings
+1. **[severity]** Description of finding
+   - Evidence from GitNexus tools
+   - Affected callers/flows
+
+### Missing Coverage
+- Callers not updated in PR: ...
+- Untested flows: ...
+
+### Recommendation
+APPROVE / REQUEST CHANGES / NEEDS DISCUSSION
+```

.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md

@@ -6,6 +6,7 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 # Refactoring with GitNexus
 
 ## When to Use
+
 - "Rename this function safely"
 - "Extract this into a module"
 - "Split this service"
@@ -26,6 +27,7 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 ## Checklists
 
 ### Rename Symbol
+
 ```
 - [ ] gitnexus_rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
 - [ ] Review graph edits (high confidence) and ast_search edits (review carefully)
@@ -35,6 +37,7 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 ```
 
 ### Extract Module
+
 ```
 - [ ] gitnexus_context({name: target}) — see all incoming/outgoing refs
 - [ ] gitnexus_impact({target, direction: "upstream"}) — find all external callers
@@ -45,6 +48,7 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 ```
 
 ### Split Function/Service
+
 ```
 - [ ] gitnexus_context({name: target}) — understand all callees
 - [ ] Group callees by responsibility
@@ -58,6 +62,7 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 ## Tools
 
 **gitnexus_rename** — automated multi-file rename:
+
 ```
 gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
 → 12 edits across 8 files
@@ -66,6 +71,7 @@ gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_
 ```
 
 **gitnexus_impact** — map all dependents first:
+
 ```
 gitnexus_impact({target: "validateUser", direction: "upstream"})
 → d=1: loginHandler, apiMiddleware, testUtils
@@ -73,6 +79,7 @@ gitnexus_impact({target: "validateUser", direction: "upstream"})
 ```
 
 **gitnexus_detect_changes** — verify your changes after refactoring:
+
 ```
 gitnexus_detect_changes({scope: "all"})
 → Changed: 8 files, 12 symbols
@@ -81,6 +88,7 @@ gitnexus_detect_changes({scope: "all"})
 ```
 
 **gitnexus_cypher** — custom reference queries:
+
 ```cypher
 MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "validateUser"})
 RETURN caller.name, caller.filePath ORDER BY caller.filePath
@@ -88,12 +96,12 @@ RETURN caller.name, caller.filePath ORDER BY caller.filePath
 
 ## Risk Rules
 
-| Risk Factor | Mitigation |
+| Risk Factor         | Mitigation                                |
-|-------------|------------|
+| ------------------- | ----------------------------------------- |
-| Many callers (>5) | Use gitnexus_rename for automated updates |
+| Many callers (>5)   | Use gitnexus_rename for automated updates |
-| Cross-area refs | Use detect_changes after to verify scope |
+| Cross-area refs     | Use detect_changes after to verify scope  |
-| String/dynamic refs | gitnexus_query to find them |
+| String/dynamic refs | gitnexus_query to find them               |
-| External/public API | Version and deprecate properly |
+| External/public API | Version and deprecate properly            |
 
 ## Example: Rename `validateUser` to `authenticateUser`
 

.github/workflows/ci.yml

@@ -1,8 +1,11 @@
 name: CI
 
 on:
+  push:
+    branches: [main]
   pull_request:
     branches: [main]
+  workflow_call:
 
 jobs:
   typecheck:
@@ -18,3 +21,49 @@ jobs:
         working-directory: gitnexus
       - run: npx tsc --noEmit
         working-directory: gitnexus
+
+  unit-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: gitnexus/package-lock.json
+      - run: npm ci
+        working-directory: gitnexus
+      - run: npx vitest run test/unit --coverage --coverage.thresholdAutoUpdate=false
+        working-directory: gitnexus
+
+  integration-tests:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: gitnexus/package-lock.json
+      - run: npm ci
+        working-directory: gitnexus
+      - run: npx vitest run test/integration
+        working-directory: gitnexus
+
+  cross-platform:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: gitnexus/package-lock.json
+      - run: npm ci
+        working-directory: gitnexus
+      - run: npx vitest run test/unit
+        working-directory: gitnexus

.github/workflows/publish.yml

@@ -6,10 +6,15 @@ on:
       - 'v*'
 
 jobs:
+  ci:
+    uses: ./.github/workflows/ci.yml
+
   publish:
+    needs: ci
     runs-on: ubuntu-latest
     permissions:
-      contents: read
+      contents: write
+      id-token: write
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-node@v4
@@ -20,9 +25,33 @@ jobs:
           cache-dependency-path: gitnexus/package-lock.json
       - run: npm ci
         working-directory: gitnexus
-      - run: npx tsc --noEmit
+
+      - name: Verify version consistency
+        run: |
+          TAG_VERSION="${GITHUB_REF#refs/tags/v}"
+          PKG_VERSION=$(node -p "require('./package.json').version")
+          if [ "$TAG_VERSION" != "$PKG_VERSION" ]; then
+            echo "::error::Tag version (v$TAG_VERSION) does not match package.json version ($PKG_VERSION)"
+            exit 1
+          fi
+          echo "Version verified: $PKG_VERSION"
         working-directory: gitnexus
-      - run: npm publish
+
+      - name: Build
+        run: npm run build
+        working-directory: gitnexus
+
+      - name: Dry-run publish
+        run: npm publish --dry-run
+        working-directory: gitnexus
+
+      - name: Publish to npm
+        run: npm publish --provenance --access public
         working-directory: gitnexus
         env:
           NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

AGENTS.md

@@ -1,14 +1,10 @@
 <!-- gitnexus:start -->
 # GitNexus MCP
 
-This project is indexed by GitNexus as **GitnexusV2** (1348 symbols, 3469 relationships, 104 execution flows).
+This project is indexed by GitNexus as **GitnexusV2** (1444 symbols, 3700 relationships, 111 execution flows).
-
-GitNexus provides a knowledge graph over this codebase — call chains, blast radius, execution flows, and semantic search.
 
 ## Always Start Here
 
-For any task involving code understanding, debugging, impact analysis, or refactoring, you must:
-
 1. **Read `gitnexus://repo/{name}/context`** — codebase overview + check index freshness
 2. **Match your task to a skill below** and **read that skill file**
 3. **Follow the skill's workflow and checklist**
@@ -23,40 +19,7 @@ For any task involving code understanding, debugging, impact analysis, or refact
 | Blast radius / "What breaks if I change X?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
 | Trace bugs / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
 | Rename / extract / split / refactor | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
+| Tools, resources, schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
+| Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
 
-## Tools Reference
+<!-- gitnexus:end -->
-
-| Tool | What it gives you |
-|------|-------------------|
-| `query` | Process-grouped code intelligence — execution flows related to a concept |
-| `context` | 360-degree symbol view — categorized refs, processes it participates in |
-| `impact` | Symbol blast radius — what breaks at depth 1/2/3 with confidence |
-| `detect_changes` | Git-diff impact — what do your current changes affect |
-| `rename` | Multi-file coordinated rename with confidence-tagged edits |
-| `cypher` | Raw graph queries (read `gitnexus://repo/{name}/schema` first) |
-| `list_repos` | Discover indexed repos |
-
-## Resources Reference
-
-Lightweight reads (~100-500 tokens) for navigation:
-
-| Resource | Content |
-|----------|---------|
-| `gitnexus://repo/{name}/context` | Stats, staleness check |
-| `gitnexus://repo/{name}/clusters` | All functional areas with cohesion scores |
-| `gitnexus://repo/{name}/cluster/{clusterName}` | Area members |
-| `gitnexus://repo/{name}/processes` | All execution flows |
-| `gitnexus://repo/{name}/process/{processName}` | Step-by-step trace |
-| `gitnexus://repo/{name}/schema` | Graph schema for Cypher |
-
-## Graph Schema
-
-**Nodes:** File, Function, Class, Interface, Method, Community, Process
-**Edges (via CodeRelation.type):** CALLS, IMPORTS, EXTENDS, IMPLEMENTS, DEFINES, MEMBER_OF, STEP_IN_PROCESS
-
-```cypher
-MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "myFunc"})
-RETURN caller.name, caller.filePath
-```
-
-<!-- gitnexus:end -->

CLAUDE.md

@@ -1,14 +1,10 @@
 <!-- gitnexus:start -->
 # GitNexus MCP
 
-This project is indexed by GitNexus as **GitnexusV2** (1348 symbols, 3469 relationships, 104 execution flows).
+This project is indexed by GitNexus as **GitnexusV2** (1444 symbols, 3700 relationships, 111 execution flows).
-
-GitNexus provides a knowledge graph over this codebase — call chains, blast radius, execution flows, and semantic search.
 
 ## Always Start Here
 
-For any task involving code understanding, debugging, impact analysis, or refactoring, you must:
-
 1. **Read `gitnexus://repo/{name}/context`** — codebase overview + check index freshness
 2. **Match your task to a skill below** and **read that skill file**
 3. **Follow the skill's workflow and checklist**
@@ -23,40 +19,7 @@ For any task involving code understanding, debugging, impact analysis, or refact
 | Blast radius / "What breaks if I change X?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
 | Trace bugs / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
 | Rename / extract / split / refactor | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
+| Tools, resources, schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
+| Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
 
-## Tools Reference
+<!-- gitnexus:end -->
-
-| Tool | What it gives you |
-|------|-------------------|
-| `query` | Process-grouped code intelligence — execution flows related to a concept |
-| `context` | 360-degree symbol view — categorized refs, processes it participates in |
-| `impact` | Symbol blast radius — what breaks at depth 1/2/3 with confidence |
-| `detect_changes` | Git-diff impact — what do your current changes affect |
-| `rename` | Multi-file coordinated rename with confidence-tagged edits |
-| `cypher` | Raw graph queries (read `gitnexus://repo/{name}/schema` first) |
-| `list_repos` | Discover indexed repos |
-
-## Resources Reference
-
-Lightweight reads (~100-500 tokens) for navigation:
-
-| Resource | Content |
-|----------|---------|
-| `gitnexus://repo/{name}/context` | Stats, staleness check |
-| `gitnexus://repo/{name}/clusters` | All functional areas with cohesion scores |
-| `gitnexus://repo/{name}/cluster/{clusterName}` | Area members |
-| `gitnexus://repo/{name}/processes` | All execution flows |
-| `gitnexus://repo/{name}/process/{processName}` | Step-by-step trace |
-| `gitnexus://repo/{name}/schema` | Graph schema for Cypher |
-
-## Graph Schema
-
-**Nodes:** File, Function, Class, Interface, Method, Community, Process
-**Edges (via CodeRelation.type):** CALLS, IMPORTS, EXTENDS, IMPLEMENTS, DEFINES, MEMBER_OF, STEP_IN_PROCESS
-
-```cypher
-MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "myFunc"})
-RETURN caller.name, caller.filePath
-```
-
-<!-- gitnexus:end -->

README.md

@@ -1,4 +1,5 @@
 # GitNexus
+⚠️ Important Notice:** GitNexus has NO official cryptocurrency, token, or coin. Any token/coin using the GitNexus name on Pump.fun or any other platform is **not affiliated with, endorsed by, or created by** this project or its maintainers. Do not purchase any cryptocurrency claiming association with GitNexus.
 
 <div align="center">
 

gitnexus-claude-plugin/.claude-plugin/plugin.json

@@ -1,11 +1,11 @@
 {
   "name": "gitnexus",
   "description": "Code intelligence powered by a knowledge graph. Provides execution flow tracing, blast radius analysis, and augmented search across your codebase.",
-  "version": "1.3.3",
+  "version": "1.3.6",
   "author": {
     "name": "GitNexus"
   },
-  "homepage": "https://github.com/nicosxt/gitnexus",
+  "homepage": "https://github.com/abhigyanpatwari/GitNexus",
-  "repository": "https://github.com/nicosxt/gitnexus",
+  "repository": "https://github.com/abhigyanpatwari/GitNexus",
   "keywords": ["code-intelligence", "knowledge-graph", "mcp", "static-analysis"]
 }

gitnexus-claude-plugin/hooks/gitnexus-hook.js

@@ -105,12 +105,14 @@ function main() {
     // stdout fd at OS level, making it unusable in subprocess contexts).
     let result = '';
 
+    const isWin = process.platform === 'win32';
+
     // Try direct gitnexus binary first (faster if globally installed)
     try {
       const child = spawnSync(
         'gitnexus',
         ['augment', pattern],
-        { encoding: 'utf-8', timeout: 8000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+        { encoding: 'utf-8', timeout: 8000, cwd, stdio: ['pipe', 'pipe', 'pipe'], shell: isWin }
       );
       if (child.status === 0 && child.stderr && child.stderr.trim()) {
         result = child.stderr;
@@ -123,7 +125,7 @@ function main() {
         const child = spawnSync(
           'npx',
           ['-y', 'gitnexus', 'augment', pattern],
-          { encoding: 'utf-8', timeout: 15000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+          { encoding: 'utf-8', timeout: 15000, cwd, stdio: ['pipe', 'pipe', 'pipe'], shell: isWin }
         );
         if (child.status === 0 && child.stderr && child.stderr.trim()) {
           result = child.stderr;

gitnexus-claude-plugin/skills/gitnexus-pr-review/SKILL.md

@@ -0,0 +1,163 @@
+---
+name: gitnexus-pr-review
+description: "Use when the user wants to review a pull request, understand what a PR changes, assess risk of merging, or check for missing test coverage. Examples: \"Review this PR\", \"What does PR #42 change?\", \"Is this PR safe to merge?\""
+---
+
+# PR Review with GitNexus
+
+## When to Use
+
+- "Review this PR"
+- "What does PR #42 change?"
+- "Is this safe to merge?"
+- "What's the blast radius of this PR?"
+- "Are there missing tests for this PR?"
+- Reviewing someone else's code changes before merge
+
+## Workflow
+
+```
+1. gh pr diff <number>                                    → Get the raw diff
+2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
+3. For each changed symbol:
+   gitnexus_impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
+4. gitnexus_context({name: "<key symbol>"})               → Understand callers/callees
+5. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
+6. Summarize findings with risk assessment
+```
+
+> If "Index is stale" → run `npx gitnexus analyze` in terminal before reviewing.
+
+## Checklist
+
+```
+- [ ] Fetch PR diff (gh pr diff or git diff base...head)
+- [ ] gitnexus_detect_changes to map changes to affected execution flows
+- [ ] gitnexus_impact on each non-trivial changed symbol
+- [ ] Review d=1 items (WILL BREAK) — are callers updated?
+- [ ] gitnexus_context on key changed symbols to understand full picture
+- [ ] Check if affected processes have test coverage
+- [ ] Assess overall risk level
+- [ ] Write review summary with findings
+```
+
+## Review Dimensions
+
+| Dimension | How GitNexus Helps |
+| --- | --- |
+| **Correctness** | `context` shows callers — are they all compatible with the change? |
+| **Blast radius** | `impact` shows d=1/d=2/d=3 dependents — anything missed? |
+| **Completeness** | `detect_changes` shows all affected flows — are they all handled? |
+| **Test coverage** | `impact({includeTests: true})` shows which tests touch changed code |
+| **Breaking changes** | d=1 upstream items that aren't updated in the PR = potential breakage |
+
+## Risk Assessment
+
+| Signal | Risk |
+| --- | --- |
+| Changes touch <3 symbols, 0-1 processes | LOW |
+| Changes touch 3-10 symbols, 2-5 processes | MEDIUM |
+| Changes touch >10 symbols or many processes | HIGH |
+| Changes touch auth, payments, or data integrity code | CRITICAL |
+| d=1 callers exist outside the PR diff | Potential breakage — flag it |
+
+## Tools
+
+**gitnexus_detect_changes** — map PR diff to affected execution flows:
+
+```
+gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+
+→ Changed: 8 symbols in 4 files
+→ Affected processes: CheckoutFlow, RefundFlow, WebhookHandler
+→ Risk: MEDIUM
+```
+
+**gitnexus_impact** — blast radius per changed symbol:
+
+```
+gitnexus_impact({target: "validatePayment", direction: "upstream"})
+
+→ d=1 (WILL BREAK):
+  - processCheckout (src/checkout.ts:42) [CALLS, 100%]
+  - webhookHandler (src/webhooks.ts:15) [CALLS, 100%]
+
+→ d=2 (LIKELY AFFECTED):
+  - checkoutRouter (src/routes/checkout.ts:22) [CALLS, 95%]
+```
+
+**gitnexus_impact with tests** — check test coverage:
+
+```
+gitnexus_impact({target: "validatePayment", direction: "upstream", includeTests: true})
+
+→ Tests that cover this symbol:
+  - validatePayment.test.ts [direct]
+  - checkout.integration.test.ts [via processCheckout]
+```
+
+**gitnexus_context** — understand a changed symbol's role:
+
+```
+gitnexus_context({name: "validatePayment"})
+
+→ Incoming calls: processCheckout, webhookHandler
+→ Outgoing calls: verifyCard, fetchRates
+→ Processes: CheckoutFlow (step 3/7), RefundFlow (step 1/5)
+```
+
+## Example: "Review PR #42"
+
+```
+1. gh pr diff 42 > /tmp/pr42.diff
+   → 4 files changed: payments.ts, checkout.ts, types.ts, utils.ts
+
+2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+   → Changed symbols: validatePayment, PaymentInput, formatAmount
+   → Affected processes: CheckoutFlow, RefundFlow
+   → Risk: MEDIUM
+
+3. gitnexus_impact({target: "validatePayment", direction: "upstream"})
+   → d=1: processCheckout, webhookHandler (WILL BREAK)
+   → webhookHandler is NOT in the PR diff — potential breakage!
+
+4. gitnexus_impact({target: "PaymentInput", direction: "upstream"})
+   → d=1: validatePayment (in PR), createPayment (NOT in PR)
+   → createPayment uses the old PaymentInput shape — breaking change!
+
+5. gitnexus_context({name: "formatAmount"})
+   → Called by 12 functions — but change is backwards-compatible (added optional param)
+
+6. Review summary:
+   - MEDIUM risk — 3 changed symbols affect 2 execution flows
+   - BUG: webhookHandler calls validatePayment but isn't updated for new signature
+   - BUG: createPayment depends on PaymentInput type which changed
+   - OK: formatAmount change is backwards-compatible
+   - Tests: checkout.test.ts covers processCheckout path, but no webhook test
+```
+
+## Review Output Format
+
+Structure your review as:
+
+```markdown
+## PR Review: <title>
+
+**Risk: LOW / MEDIUM / HIGH / CRITICAL**
+
+### Changes Summary
+- <N> symbols changed across <M> files
+- <P> execution flows affected
+
+### Findings
+1. **[severity]** Description of finding
+   - Evidence from GitNexus tools
+   - Affected callers/flows
+
+### Missing Coverage
+- Callers not updated in PR: ...
+- Untested flows: ...
+
+### Recommendation
+APPROVE / REQUEST CHANGES / NEEDS DISCUSSION
+```

gitnexus-cursor-integration/skills/gitnexus-pr-review/SKILL.md

@@ -0,0 +1,163 @@
+---
+name: gitnexus-pr-review
+description: "Use when the user wants to review a pull request, understand what a PR changes, assess risk of merging, or check for missing test coverage. Examples: \"Review this PR\", \"What does PR #42 change?\", \"Is this PR safe to merge?\""
+---
+
+# PR Review with GitNexus
+
+## When to Use
+
+- "Review this PR"
+- "What does PR #42 change?"
+- "Is this safe to merge?"
+- "What's the blast radius of this PR?"
+- "Are there missing tests for this PR?"
+- Reviewing someone else's code changes before merge
+
+## Workflow
+
+```
+1. gh pr diff <number>                                    → Get the raw diff
+2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
+3. For each changed symbol:
+   gitnexus_impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
+4. gitnexus_context({name: "<key symbol>"})               → Understand callers/callees
+5. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
+6. Summarize findings with risk assessment
+```
+
+> If "Index is stale" → run `npx gitnexus analyze` in terminal before reviewing.
+
+## Checklist
+
+```
+- [ ] Fetch PR diff (gh pr diff or git diff base...head)
+- [ ] gitnexus_detect_changes to map changes to affected execution flows
+- [ ] gitnexus_impact on each non-trivial changed symbol
+- [ ] Review d=1 items (WILL BREAK) — are callers updated?
+- [ ] gitnexus_context on key changed symbols to understand full picture
+- [ ] Check if affected processes have test coverage
+- [ ] Assess overall risk level
+- [ ] Write review summary with findings
+```
+
+## Review Dimensions
+
+| Dimension | How GitNexus Helps |
+| --- | --- |
+| **Correctness** | `context` shows callers — are they all compatible with the change? |
+| **Blast radius** | `impact` shows d=1/d=2/d=3 dependents — anything missed? |
+| **Completeness** | `detect_changes` shows all affected flows — are they all handled? |
+| **Test coverage** | `impact({includeTests: true})` shows which tests touch changed code |
+| **Breaking changes** | d=1 upstream items that aren't updated in the PR = potential breakage |
+
+## Risk Assessment
+
+| Signal | Risk |
+| --- | --- |
+| Changes touch <3 symbols, 0-1 processes | LOW |
+| Changes touch 3-10 symbols, 2-5 processes | MEDIUM |
+| Changes touch >10 symbols or many processes | HIGH |
+| Changes touch auth, payments, or data integrity code | CRITICAL |
+| d=1 callers exist outside the PR diff | Potential breakage — flag it |
+
+## Tools
+
+**gitnexus_detect_changes** — map PR diff to affected execution flows:
+
+```
+gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+
+→ Changed: 8 symbols in 4 files
+→ Affected processes: CheckoutFlow, RefundFlow, WebhookHandler
+→ Risk: MEDIUM
+```
+
+**gitnexus_impact** — blast radius per changed symbol:
+
+```
+gitnexus_impact({target: "validatePayment", direction: "upstream"})
+
+→ d=1 (WILL BREAK):
+  - processCheckout (src/checkout.ts:42) [CALLS, 100%]
+  - webhookHandler (src/webhooks.ts:15) [CALLS, 100%]
+
+→ d=2 (LIKELY AFFECTED):
+  - checkoutRouter (src/routes/checkout.ts:22) [CALLS, 95%]
+```
+
+**gitnexus_impact with tests** — check test coverage:
+
+```
+gitnexus_impact({target: "validatePayment", direction: "upstream", includeTests: true})
+
+→ Tests that cover this symbol:
+  - validatePayment.test.ts [direct]
+  - checkout.integration.test.ts [via processCheckout]
+```
+
+**gitnexus_context** — understand a changed symbol's role:
+
+```
+gitnexus_context({name: "validatePayment"})
+
+→ Incoming calls: processCheckout, webhookHandler
+→ Outgoing calls: verifyCard, fetchRates
+→ Processes: CheckoutFlow (step 3/7), RefundFlow (step 1/5)
+```
+
+## Example: "Review PR #42"
+
+```
+1. gh pr diff 42 > /tmp/pr42.diff
+   → 4 files changed: payments.ts, checkout.ts, types.ts, utils.ts
+
+2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+   → Changed symbols: validatePayment, PaymentInput, formatAmount
+   → Affected processes: CheckoutFlow, RefundFlow
+   → Risk: MEDIUM
+
+3. gitnexus_impact({target: "validatePayment", direction: "upstream"})
+   → d=1: processCheckout, webhookHandler (WILL BREAK)
+   → webhookHandler is NOT in the PR diff — potential breakage!
+
+4. gitnexus_impact({target: "PaymentInput", direction: "upstream"})
+   → d=1: validatePayment (in PR), createPayment (NOT in PR)
+   → createPayment uses the old PaymentInput shape — breaking change!
+
+5. gitnexus_context({name: "formatAmount"})
+   → Called by 12 functions — but change is backwards-compatible (added optional param)
+
+6. Review summary:
+   - MEDIUM risk — 3 changed symbols affect 2 execution flows
+   - BUG: webhookHandler calls validatePayment but isn't updated for new signature
+   - BUG: createPayment depends on PaymentInput type which changed
+   - OK: formatAmount change is backwards-compatible
+   - Tests: checkout.test.ts covers processCheckout path, but no webhook test
+```
+
+## Review Output Format
+
+Structure your review as:
+
+```markdown
+## PR Review: <title>
+
+**Risk: LOW / MEDIUM / HIGH / CRITICAL**
+
+### Changes Summary
+- <N> symbols changed across <M> files
+- <P> execution flows affected
+
+### Findings
+1. **[severity]** Description of finding
+   - Evidence from GitNexus tools
+   - Affected callers/flows
+
+### Missing Coverage
+- Callers not updated in PR: ...
+- Untested flows: ...
+
+### Recommendation
+APPROVE / REQUEST CHANGES / NEEDS DISCUSSION
+```

gitnexus/hooks/claude/gitnexus-hook.cjs

@@ -101,20 +101,40 @@ function main() {
     const pattern = extractPattern(toolName, toolInput);
     if (!pattern || pattern.length < 3) return;
 
-    // Resolve CLI path relative to this hook script (same package)
+    // Resolve CLI path — try multiple strategies:
-    // hooks/claude/gitnexus-hook.cjs → dist/cli/index.js
+    // 1. Relative path (works when script is inside npm package)
-    const cliPath = path.resolve(__dirname, '..', '..', 'dist', 'cli', 'index.js');
+    // 2. require.resolve (works when gitnexus is globally installed)
+    // 3. Fall back to npx (works when neither is available)
+    let cliPath = path.resolve(__dirname, '..', '..', 'dist', 'cli', 'index.js');
+    if (!fs.existsSync(cliPath)) {
+      try {
+        cliPath = require.resolve('gitnexus/dist/cli/index.js');
+      } catch {
+        cliPath = ''; // will use npx fallback
+      }
+    }
 
     // augment CLI writes result to stderr (KuzuDB's native module captures
     // stdout fd at OS level, making it unusable in subprocess contexts).
     const { spawnSync } = require('child_process');
     let result = '';
     try {
-      const child = spawnSync(
+      let child;
-        process.execPath,
+      if (cliPath) {
-        [cliPath, 'augment', pattern],
+        child = spawnSync(
-        { encoding: 'utf-8', timeout: 8000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+          process.execPath,
-      );
+          [cliPath, 'augment', pattern],
+          { encoding: 'utf-8', timeout: 8000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+        );
+      } else {
+        // npx fallback
+        const cmd = process.platform === 'win32' ? 'npx.cmd' : 'npx';
+        child = spawnSync(
+          cmd,
+          ['-y', 'gitnexus', 'augment', pattern],
+          { encoding: 'utf-8', timeout: 15000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+        );
+      }
       result = child.stderr || '';
     } catch { /* graceful failure */ }
 

gitnexus/hooks/claude/pre-tool-use.sh

@@ -63,7 +63,8 @@ if [ "$found" = false ]; then
 fi
 
 # Run gitnexus augment — must be fast (<500ms target)
-RESULT=$(cd "$CWD" && npx -y gitnexus augment "$PATTERN" 2>/dev/null)
+# augment writes to stderr (KuzuDB captures stdout at OS level), so capture stderr and discard stdout
+RESULT=$(cd "$CWD" && npx -y gitnexus augment "$PATTERN" 2>&1 1>/dev/null)
 
 if [ -n "$RESULT" ]; then
   ESCAPED=$(echo "$RESULT" | jq -Rs .)

gitnexus/package.json

@@ -39,6 +39,11 @@
   "scripts": {
     "build": "tsc",
     "dev": "tsx watch src/cli/index.ts",
+    "test": "vitest run test/unit",
+    "test:integration": "vitest run test/integration",
+    "test:all": "vitest run",
+    "test:watch": "vitest",
+    "test:coverage": "vitest run --coverage",
     "prepare": "npm run build",
     "postinstall": "node scripts/patch-tree-sitter-swift.cjs"
   },
@@ -69,7 +74,6 @@
     "tree-sitter-python": "^0.21.0",
     "tree-sitter-rust": "^0.21.0",
     "tree-sitter-typescript": "^0.21.0",
-    "typescript": "^5.4.5",
     "uuid": "^13.0.0"
   },
   "optionalDependencies": {
@@ -81,7 +85,10 @@
     "@types/express": "^4.17.21",
     "@types/node": "^20.0.0",
     "@types/uuid": "^10.0.0",
-    "tsx": "^4.0.0"
+    "@vitest/coverage-v8": "^4.0.18",
+    "tsx": "^4.0.0",
+    "typescript": "^5.4.5",
+    "vitest": "^4.0.18"
   },
   "engines": {
     "node": ">=18.0.0"

gitnexus/skills/gitnexus-pr-review.md

@@ -0,0 +1,163 @@
+---
+name: gitnexus-pr-review
+description: "Use when the user wants to review a pull request, understand what a PR changes, assess risk of merging, or check for missing test coverage. Examples: \"Review this PR\", \"What does PR #42 change?\", \"Is this PR safe to merge?\""
+---
+
+# PR Review with GitNexus
+
+## When to Use
+
+- "Review this PR"
+- "What does PR #42 change?"
+- "Is this safe to merge?"
+- "What's the blast radius of this PR?"
+- "Are there missing tests for this PR?"
+- Reviewing someone else's code changes before merge
+
+## Workflow
+
+```
+1. gh pr diff <number>                                    → Get the raw diff
+2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})  → Map diff to affected flows
+3. For each changed symbol:
+   gitnexus_impact({target: "<symbol>", direction: "upstream"})    → Blast radius per change
+4. gitnexus_context({name: "<key symbol>"})               → Understand callers/callees
+5. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
+6. Summarize findings with risk assessment
+```
+
+> If "Index is stale" → run `npx gitnexus analyze` in terminal before reviewing.
+
+## Checklist
+
+```
+- [ ] Fetch PR diff (gh pr diff or git diff base...head)
+- [ ] gitnexus_detect_changes to map changes to affected execution flows
+- [ ] gitnexus_impact on each non-trivial changed symbol
+- [ ] Review d=1 items (WILL BREAK) — are callers updated?
+- [ ] gitnexus_context on key changed symbols to understand full picture
+- [ ] Check if affected processes have test coverage
+- [ ] Assess overall risk level
+- [ ] Write review summary with findings
+```
+
+## Review Dimensions
+
+| Dimension | How GitNexus Helps |
+| --- | --- |
+| **Correctness** | `context` shows callers — are they all compatible with the change? |
+| **Blast radius** | `impact` shows d=1/d=2/d=3 dependents — anything missed? |
+| **Completeness** | `detect_changes` shows all affected flows — are they all handled? |
+| **Test coverage** | `impact({includeTests: true})` shows which tests touch changed code |
+| **Breaking changes** | d=1 upstream items that aren't updated in the PR = potential breakage |
+
+## Risk Assessment
+
+| Signal | Risk |
+| --- | --- |
+| Changes touch <3 symbols, 0-1 processes | LOW |
+| Changes touch 3-10 symbols, 2-5 processes | MEDIUM |
+| Changes touch >10 symbols or many processes | HIGH |
+| Changes touch auth, payments, or data integrity code | CRITICAL |
+| d=1 callers exist outside the PR diff | Potential breakage — flag it |
+
+## Tools
+
+**gitnexus_detect_changes** — map PR diff to affected execution flows:
+
+```
+gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+
+→ Changed: 8 symbols in 4 files
+→ Affected processes: CheckoutFlow, RefundFlow, WebhookHandler
+→ Risk: MEDIUM
+```
+
+**gitnexus_impact** — blast radius per changed symbol:
+
+```
+gitnexus_impact({target: "validatePayment", direction: "upstream"})
+
+→ d=1 (WILL BREAK):
+  - processCheckout (src/checkout.ts:42) [CALLS, 100%]
+  - webhookHandler (src/webhooks.ts:15) [CALLS, 100%]
+
+→ d=2 (LIKELY AFFECTED):
+  - checkoutRouter (src/routes/checkout.ts:22) [CALLS, 95%]
+```
+
+**gitnexus_impact with tests** — check test coverage:
+
+```
+gitnexus_impact({target: "validatePayment", direction: "upstream", includeTests: true})
+
+→ Tests that cover this symbol:
+  - validatePayment.test.ts [direct]
+  - checkout.integration.test.ts [via processCheckout]
+```
+
+**gitnexus_context** — understand a changed symbol's role:
+
+```
+gitnexus_context({name: "validatePayment"})
+
+→ Incoming calls: processCheckout, webhookHandler
+→ Outgoing calls: verifyCard, fetchRates
+→ Processes: CheckoutFlow (step 3/7), RefundFlow (step 1/5)
+```
+
+## Example: "Review PR #42"
+
+```
+1. gh pr diff 42 > /tmp/pr42.diff
+   → 4 files changed: payments.ts, checkout.ts, types.ts, utils.ts
+
+2. gitnexus_detect_changes({scope: "compare", base_ref: "main"})
+   → Changed symbols: validatePayment, PaymentInput, formatAmount
+   → Affected processes: CheckoutFlow, RefundFlow
+   → Risk: MEDIUM
+
+3. gitnexus_impact({target: "validatePayment", direction: "upstream"})
+   → d=1: processCheckout, webhookHandler (WILL BREAK)
+   → webhookHandler is NOT in the PR diff — potential breakage!
+
+4. gitnexus_impact({target: "PaymentInput", direction: "upstream"})
+   → d=1: validatePayment (in PR), createPayment (NOT in PR)
+   → createPayment uses the old PaymentInput shape — breaking change!
+
+5. gitnexus_context({name: "formatAmount"})
+   → Called by 12 functions — but change is backwards-compatible (added optional param)
+
+6. Review summary:
+   - MEDIUM risk — 3 changed symbols affect 2 execution flows
+   - BUG: webhookHandler calls validatePayment but isn't updated for new signature
+   - BUG: createPayment depends on PaymentInput type which changed
+   - OK: formatAmount change is backwards-compatible
+   - Tests: checkout.test.ts covers processCheckout path, but no webhook test
+```
+
+## Review Output Format
+
+Structure your review as:
+
+```markdown
+## PR Review: <title>
+
+**Risk: LOW / MEDIUM / HIGH / CRITICAL**
+
+### Changes Summary
+- <N> symbols changed across <M> files
+- <P> execution flows affected
+
+### Findings
+1. **[severity]** Description of finding
+   - Evidence from GitNexus tools
+   - Affected callers/flows
+
+### Missing Coverage
+- Callers not updated in PR: ...
+- Untested flows: ...
+
+### Recommendation
+APPROVE / REQUEST CHANGES / NEEDS DISCUSSION
+```

gitnexus/src/cli/ai-context.ts

@@ -100,7 +100,7 @@ async function upsertGitNexusSection(
   const startIdx = existingContent.indexOf(GITNEXUS_START_MARKER);
   const endIdx = existingContent.indexOf(GITNEXUS_END_MARKER);
 
-  if (startIdx !== -1 && endIdx !== -1) {
+  if (startIdx !== -1 && endIdx !== -1 && endIdx > startIdx) {
     // Replace existing section
     const before = existingContent.substring(0, startIdx);
     const after = existingContent.substring(endIdx + GITNEXUS_END_MARKER.length);

gitnexus/src/cli/analyze.ts

@@ -18,7 +18,7 @@ import { getStoragePaths, saveMeta, loadMeta, addToGitignore, registerRepo, getG
 import { getCurrentCommit, isGitRepo, getGitRoot } from '../storage/git.js';
 import { generateAIContextFiles } from './ai-context.js';
 import fs from 'fs/promises';
-import { registerClaudeHook } from './claude-hooks.js';
+
 
 const HEAP_MB = 8192;
 const HEAP_FLAG = `--max-old-space-size=${HEAP_MB}`;
@@ -292,8 +292,6 @@ export const analyzeCommand = async (
   await registerRepo(repoPath, meta);
   await addToGitignore(repoPath);
 
-  const hookResult = await registerClaudeHook();
-
   const projectName = path.basename(repoPath);
   let aggregatedClusterCount = 0;
   if (pipelineResult.communityResult?.communities) {
@@ -342,10 +340,6 @@ export const analyzeCommand = async (
     console.log(`  Context: ${aiContext.files.join(', ')}`);
   }
 
-  if (hookResult.registered) {
-    console.log(`  Hooks: ${hookResult.message}`);
-  }
-
   // Show a quiet summary if some edge types needed fallback insertion
   if (kuzuWarnings.length > 0) {
     const totalFallback = kuzuWarnings.reduce((sum, w) => {

gitnexus/src/cli/claude-hooks.ts

@@ -1,111 +0,0 @@
-/**
- * Claude Code Hook Registration
- * 
- * Registers the GitNexus PreToolUse hook in ~/.claude/hooks.json
- * so that grep/glob/bash calls are automatically augmented with
- * knowledge graph context.
- * 
- * Idempotent — safe to call multiple times.
- */
-
-import fs from 'fs/promises';
-import path from 'path';
-import os from 'os';
-import { fileURLToPath } from 'url';
-
-const __filename = fileURLToPath(import.meta.url);
-const __dirname = path.dirname(__filename);
-
-/**
- * Get the absolute path to the gitnexus-hook.js file.
- * Works for both local dev and npm-installed packages.
- */
-function getHookScriptPath(): string {
-  // From dist/cli/claude-hooks.js → hooks/claude/gitnexus-hook.js
-  const packageRoot = path.resolve(__dirname, '..', '..');
-  return path.join(packageRoot, 'hooks', 'claude', 'gitnexus-hook.cjs');
-}
-
-/**
- * Register (or verify) the GitNexus hook in Claude Code's global hooks.json.
- * 
- * - Creates ~/.claude/ and hooks.json if they don't exist
- * - Preserves existing hooks from other tools
- * - Skips if GitNexus hook is already registered
- * 
- * Returns a status message for the CLI output.
- */
-export async function registerClaudeHook(): Promise<{ registered: boolean; message: string }> {
-  const claudeDir = path.join(os.homedir(), '.claude');
-  const hooksFile = path.join(claudeDir, 'hooks.json');
-  const hookScript = getHookScriptPath();
-  
-  // Check if the hook script exists
-  try {
-    await fs.access(hookScript);
-  } catch {
-    return { registered: false, message: 'Hook script not found (package may be incomplete)' };
-  }
-
-  // Build the hook command — use node + absolute path for reliability
-  const hookCommand = `node "${hookScript}"`;
-  
-  // Check if ~/.claude/ exists (user has Claude Code installed)
-  try {
-    await fs.access(claudeDir);
-  } catch {
-    // No Claude Code installation — skip silently
-    return { registered: false, message: 'Claude Code not detected (~/.claude/ not found)' };
-  }
-  
-  // Read existing hooks.json or start fresh
-  let hooksConfig: any = {};
-  try {
-    const existing = await fs.readFile(hooksFile, 'utf-8');
-    hooksConfig = JSON.parse(existing);
-  } catch {
-    // File doesn't exist or is invalid — we'll create it
-  }
-  
-  // Ensure the hooks structure exists
-  if (!hooksConfig.hooks) {
-    hooksConfig.hooks = {};
-  }
-  if (!Array.isArray(hooksConfig.hooks.PreToolUse)) {
-    hooksConfig.hooks.PreToolUse = [];
-  }
-  
-  // Check if GitNexus hook is already registered
-  const existingEntry = hooksConfig.hooks.PreToolUse.find((entry: any) => {
-    if (!entry.hooks || !Array.isArray(entry.hooks)) return false;
-    return entry.hooks.some((h: any) => 
-      h.command && (
-        h.command.includes('gitnexus-hook') || 
-        h.command.includes('gitnexus augment')
-      )
-    );
-  });
-  
-  if (existingEntry) {
-    return { registered: true, message: 'Claude Code hook already registered' };
-  }
-  
-  // Add the GitNexus hook entry
-  hooksConfig.hooks.PreToolUse.push({
-    matcher: {
-      tool_name: "Grep|Glob|Bash"
-    },
-    hooks: [
-      {
-        type: "command",
-        command: hookCommand,
-        timeout: 8000
-      }
-    ]
-  });
-  
-  // Write back
-  await fs.writeFile(hooksFile, JSON.stringify(hooksConfig, null, 2) + '\n', 'utf-8');
-  
-  return { registered: true, message: 'Claude Code hook registered' };
-}

gitnexus/src/cli/eval-server.ts

@@ -36,7 +36,7 @@ export interface EvalServerOptions {
 // Convert structured JSON results into compact, LLM-friendly text.
 // Design: minimize tokens, maximize actionability.
 
-function formatQueryResult(result: any): string {
+export function formatQueryResult(result: any): string {
   if (result.error) return `Error: ${result.error}`;
 
   const lines: string[] = [];
@@ -77,7 +77,7 @@ function formatQueryResult(result: any): string {
   return lines.join('\n').trim();
 }
 
-function formatContextResult(result: any): string {
+export function formatContextResult(result: any): string {
   if (result.error) return `Error: ${result.error}`;
 
   if (result.status === 'ambiguous') {
@@ -141,7 +141,7 @@ function formatContextResult(result: any): string {
   return lines.join('\n').trim();
 }
 
-function formatImpactResult(result: any): string {
+export function formatImpactResult(result: any): string {
   if (result.error) return `Error: ${result.error}`;
 
   const target = result.target;
@@ -181,7 +181,7 @@ function formatImpactResult(result: any): string {
   return lines.join('\n').trim();
 }
 
-function formatCypherResult(result: any): string {
+export function formatCypherResult(result: any): string {
   if (result.error) return `Error: ${result.error}`;
 
   if (Array.isArray(result)) {
@@ -202,7 +202,7 @@ function formatCypherResult(result: any): string {
   return typeof result === 'string' ? result : JSON.stringify(result, null, 2);
 }
 
-function formatDetectChangesResult(result: any): string {
+export function formatDetectChangesResult(result: any): string {
   if (result.error) return `Error: ${result.error}`;
 
   const summary = result.summary || {};
@@ -238,7 +238,7 @@ function formatDetectChangesResult(result: any): string {
   return lines.join('\n').trim();
 }
 
-function formatListReposResult(result: any): string {
+export function formatListReposResult(result: any): string {
   if (!Array.isArray(result) || result.length === 0) {
     return 'No indexed repositories.';
   }
@@ -420,10 +420,20 @@ export async function evalServerCommand(options?: EvalServerOptions): Promise<vo
   process.on('SIGTERM', shutdown);
 }
 
+export const MAX_BODY_SIZE = 1024 * 1024; // 1MB
+
 function readBody(req: http.IncomingMessage): Promise<string> {
   return new Promise((resolve, reject) => {
     const chunks: Buffer[] = [];
-    req.on('data', (chunk: Buffer) => chunks.push(chunk));
+    let totalSize = 0;
+    req.on('data', (chunk: Buffer) => {
+      totalSize += chunk.length;
+      if (totalSize > MAX_BODY_SIZE) {
+        req.destroy(new Error('Request body too large (max 1MB)'));
+        return;
+      }
+      chunks.push(chunk);
+    });
     req.on('end', () => resolve(Buffer.concat(chunks).toString('utf-8')));
     req.on('error', reject);
   });

gitnexus/src/cli/index.ts

@@ -1,24 +1,7 @@
 #!/usr/bin/env node
 
-// Raise Node heap limit for large repos (e.g. Linux kernel).
+// Heap re-spawn removed — only analyze.ts needs the 8GB heap (via its own ensureHeap()).
-// Must run before any heavy allocation. If already set by the user, respect it.
+// Removing it from here improves MCP server startup time significantly.
-if (!process.env.NODE_OPTIONS?.includes('--max-old-space-size')) {
-  const execArgv = process.execArgv.join(' ');
-  if (!execArgv.includes('--max-old-space-size')) {
-    // Re-spawn with a larger heap (8 GB)
-    const { execFileSync } = await import('node:child_process');
-    try {
-      execFileSync(process.execPath, ['--max-old-space-size=8192', ...process.argv.slice(1)], {
-        stdio: 'inherit',
-        env: { ...process.env, NODE_OPTIONS: `${process.env.NODE_OPTIONS || ''} --max-old-space-size=8192`.trim() },
-      });
-      process.exit(0);
-    } catch (e: any) {
-      // If the child exited with an error code, propagate it
-      process.exit(e.status ?? 1);
-    }
-  }
-}
 
 import { Command } from 'commander';
 import { analyzeCommand } from './analyze.js';

gitnexus/src/cli/mcp.ts

@@ -14,6 +14,8 @@ export const mcpCommand = async () => {
   // KuzuDB lock conflicts and transient errors should degrade gracefully.
   process.on('uncaughtException', (err) => {
     console.error(`GitNexus MCP: uncaught exception — ${err.message}`);
+    // Process is in an undefined state after uncaughtException — exit after flushing
+    setTimeout(() => process.exit(1), 100);
   });
   process.on('unhandledRejection', (reason) => {
     const msg = reason instanceof Error ? reason.message : String(reason);

gitnexus/src/cli/setup.ts

@@ -163,7 +163,15 @@ async function installClaudeCodeHooks(result: SetupResult): Promise<void> {
     const src = path.join(pluginHooksPath, 'gitnexus-hook.cjs');
     const dest = path.join(destHooksDir, 'gitnexus-hook.cjs');
     try {
-      const content = await fs.readFile(src, 'utf-8');
+      let content = await fs.readFile(src, 'utf-8');
+      // Inject resolved CLI path so the copied hook can find the CLI
+      // even when it's no longer inside the npm package tree
+      const resolvedCli = path.join(__dirname, '..', 'cli', 'index.js');
+      const normalizedCli = path.resolve(resolvedCli).replace(/\\/g, '/');
+      content = content.replace(
+        "let cliPath = path.resolve(__dirname, '..', '..', 'dist', 'cli', 'index.js');",
+        `let cliPath = '${normalizedCli}';`
+      );
       await fs.writeFile(dest, content, 'utf-8');
     } catch {
       // Script not found in source — skip

gitnexus/src/core/ingestion/parsing-processor.ts

@@ -63,7 +63,7 @@ const getDefinitionNodeFromCaptures = (captureMap: Record<string, any>): any | n
  * @param language - The programming language
  * @returns true if the symbol is exported/public
  */
-const isNodeExported = (node: any, name: string, language: string): boolean => {
+export const isNodeExported = (node: any, name: string, language: string): boolean => {
   let current = node;
 
   switch (language) {
@@ -175,6 +175,22 @@ const isNodeExported = (node: any, name: string, language: string): boolean => {
       }
       return false;
 
+    // PHP: Check for visibility modifier or top-level scope
+    case 'php':
+      while (current) {
+        if (current.type === 'class_declaration' ||
+            current.type === 'interface_declaration' ||
+            current.type === 'trait_declaration' ||
+            current.type === 'enum_declaration') {
+          return true;
+        }
+        if (current.type === 'visibility_modifier') {
+          return current.text === 'public';
+        }
+        current = current.parent;
+      }
+      return true; // Top-level functions are globally accessible
+
     default:
       return false;
   }
@@ -314,9 +330,9 @@ const processParsingSequential = async (
       }
 
       const nameNode = captureMap['name'];
-      if (!nameNode) return;
+      // Synthesize name for constructors without explicit @name capture (e.g. Swift init)
-
+      if (!nameNode && !captureMap['definition.constructor']) return;
-      const nodeName = nameNode.text;
+      const nodeName = nameNode ? nameNode.text : 'init';
 
       let nodeLabel = 'CodeElement';
 
@@ -343,7 +359,9 @@ const processParsingSequential = async (
       else if (captureMap['definition.constructor']) nodeLabel = 'Constructor';
       else if (captureMap['definition.template']) nodeLabel = 'Template';
 
-      const nodeId = generateId(nodeLabel, `${file.path}:${nodeName}`);
+      const definitionNodeForRange = getDefinitionNodeFromCaptures(captureMap);
+      const startLine = definitionNodeForRange ? definitionNodeForRange.startPosition.row : (nameNode ? nameNode.startPosition.row : 0);
+      const nodeId = generateId(nodeLabel, `${file.path}:${nodeName}:${startLine}`);
 
       const definitionNode = getDefinitionNodeFromCaptures(captureMap);
       const frameworkHint = definitionNode
@@ -356,10 +374,10 @@ const processParsingSequential = async (
         properties: {
           name: nodeName,
           filePath: file.path,
-          startLine: nameNode.startPosition.row,
+          startLine: definitionNodeForRange ? definitionNodeForRange.startPosition.row : startLine,
-          endLine: nameNode.endPosition.row,
+          endLine: definitionNodeForRange ? definitionNodeForRange.endPosition.row : startLine,
           language: language,
-          isExported: isNodeExported(nameNode, nodeName, language),
+          isExported: isNodeExported(nameNode || definitionNodeForRange, nodeName, language),
           ...(frameworkHint ? {
             astFrameworkMultiplier: frameworkHint.entryPointMultiplier,
             astFrameworkReason: frameworkHint.reason,

gitnexus/src/core/ingestion/process-processor.ts

@@ -344,8 +344,7 @@ const traceFromEntryPoint = (
   // BFS with path tracking
   // Each queue item: [currentNodeId, pathSoFar]
   const queue: [string, string[]][] = [[entryId, [entryId]]];
-  const visited = new Set<string>();
+
-  
   while (queue.length > 0 && traces.length < config.maxBranching * 3) {
     const [currentId, path] = queue.shift()!;
     

gitnexus/src/core/ingestion/workers/parse-worker.ts

@@ -798,8 +798,12 @@ const processFileGroup = (
       if (!nodeLabel) continue;
 
       const nameNode = captureMap['name'];
-      const nodeName = nameNode.text;
+      // Synthesize name for constructors without explicit @name capture (e.g. Swift init)
-      const nodeId = generateId(nodeLabel, `${file.path}:${nodeName}`);
+      if (!nameNode && nodeLabel !== 'Constructor') continue;
+      const nodeName = nameNode ? nameNode.text : 'init';
+      const definitionNode = getDefinitionNodeFromCaptures(captureMap);
+      const startLine = definitionNode ? definitionNode.startPosition.row : (nameNode ? nameNode.startPosition.row : 0);
+      const nodeId = generateId(nodeLabel, `${file.path}:${nodeName}:${startLine}`);
 
       let description: string | undefined;
       if (language === SupportedLanguages.PHP) {
@@ -810,7 +814,6 @@ const processFileGroup = (
         }
       }
 
-      const definitionNode = getDefinitionNodeFromCaptures(captureMap);
       const frameworkHint = definitionNode
         ? detectFrameworkFromAST(language, (definitionNode.text || '').slice(0, 300))
         : null;
@@ -821,10 +824,10 @@ const processFileGroup = (
         properties: {
           name: nodeName,
           filePath: file.path,
-          startLine: nameNode.startPosition.row,
+          startLine: definitionNode ? definitionNode.startPosition.row : startLine,
-          endLine: nameNode.endPosition.row,
+          endLine: definitionNode ? definitionNode.endPosition.row : startLine,
           language: language,
-          isExported: isNodeExported(nameNode, nodeName, language),
+          isExported: isNodeExported(nameNode || definitionNode, nodeName, language),
           ...(frameworkHint ? {
             astFrameworkMultiplier: frameworkHint.entryPointMultiplier,
             astFrameworkReason: frameworkHint.reason,

gitnexus/src/core/kuzu/csv-generator.ts

@@ -25,7 +25,7 @@ const FLUSH_EVERY = 500;
 // CSV ESCAPE UTILITIES
 // ============================================================================
 
-const sanitizeUTF8 = (str: string): string => {
+export const sanitizeUTF8 = (str: string): string => {
   return str
     .replace(/\r\n/g, '\n')
     .replace(/\r/g, '\n')
@@ -34,14 +34,14 @@ const sanitizeUTF8 = (str: string): string => {
     .replace(/[\uFFFE\uFFFF]/g, '');
 };
 
-const escapeCSVField = (value: string | number | undefined | null): string => {
+export const escapeCSVField = (value: string | number | undefined | null): string => {
   if (value === undefined || value === null) return '""';
   let str = String(value);
   str = sanitizeUTF8(str);
   return `"${str.replace(/"/g, '""')}"`;
 };
 
-const escapeCSVNumber = (value: number | undefined | null, defaultValue: number = -1): string => {
+export const escapeCSVNumber = (value: number | undefined | null, defaultValue: number = -1): string => {
   if (value === undefined || value === null) return String(defaultValue);
   return String(value);
 };
@@ -50,7 +50,7 @@ const escapeCSVNumber = (value: number | undefined | null, defaultValue: number
 // CONTENT EXTRACTION (lazy — reads from disk on demand)
 // ============================================================================
 
-const isBinaryContent = (content: string): boolean => {
+export const isBinaryContent = (content: string): boolean => {
   if (!content || content.length === 0) return false;
   const sample = content.slice(0, 1000);
   let nonPrintable = 0;
@@ -80,7 +80,15 @@ class FileContentCache {
   async get(relativePath: string): Promise<string> {
     if (!relativePath) return '';
     const cached = this.cache.get(relativePath);
-    if (cached !== undefined) return cached;
+    if (cached !== undefined) {
+      // Move to end of accessOrder (LRU promotion)
+      const idx = this.accessOrder.indexOf(relativePath);
+      if (idx !== -1) {
+        this.accessOrder.splice(idx, 1);
+        this.accessOrder.push(relativePath);
+      }
+      return cached;
+    }
     try {
       const fullPath = path.join(this.repoPath, relativePath);
       const content = await fs.readFile(fullPath, 'utf-8');
@@ -163,9 +171,17 @@ class BufferedCSVWriter {
     const chunk = this.buffer.join('\n') + '\n';
     this.buffer.length = 0;
     return new Promise((resolve, reject) => {
+      this.ws.once('error', reject);
       const ok = this.ws.write(chunk);
-      if (ok) resolve();
+      if (ok) {
-      else this.ws.once('drain', resolve);
+        this.ws.removeListener('error', reject);
+        resolve();
+      } else {
+        this.ws.once('drain', () => {
+          this.ws.removeListener('error', reject);
+          resolve();
+        });
+      }
     });
   }
 
@@ -264,7 +280,7 @@ export const streamAllCSVsToDisk = async (
         break;
       case 'Community': {
         const keywords = (node.properties as any).keywords || [];
-        const keywordsStr = `[${keywords.map((k: string) => `'${k.replace(/'/g, "''")}'`).join(',')}]`;
+        const keywordsStr = `[${keywords.map((k: string) => `'${k.replace(/\\/g, '\\\\').replace(/'/g, "''").replace(/,/g, '\\,')}'`).join(',')}]`;
         await communityWriter.addRow([
           escapeCSVField(node.id),
           escapeCSVField(node.properties.name || ''),

gitnexus/src/core/kuzu/kuzu-adapter.ts

@@ -684,10 +684,15 @@ export const loadFTSExtension = async (): Promise<void> => {
   try {
     await conn.query('INSTALL fts');
     await conn.query('LOAD EXTENSION fts');
-  } catch {
+    ftsLoaded = true;
-    // Extension may already be loaded
+  } catch (err: any) {
+    const msg = err?.message || '';
+    if (msg.includes('already loaded') || msg.includes('already installed') || msg.includes('already exists')) {
+      ftsLoaded = true;
+    } else {
+      console.error('GitNexus: FTS extension load failed:', msg);
+    }
   }
-  ftsLoaded = true;
 };
 
 /**

gitnexus/src/mcp/core/kuzu-adapter.ts

@@ -42,6 +42,10 @@ const INITIAL_CONNS_PER_REPO = 2;
 
 let idleTimer: ReturnType<typeof setInterval> | null = null;
 
+/** Saved real stdout.write — used to silence KuzuDB native output without race conditions */
+const realStdoutWrite = process.stdout.write.bind(process.stdout);
+let stdoutSilenceCount = 0;
+
 /**
  * Start the idle cleanup timer (runs every 60s)
  */
@@ -50,7 +54,7 @@ function ensureIdleTimer(): void {
   idleTimer = setInterval(() => {
     const now = Date.now();
     for (const [repoId, entry] of pool) {
-      if (now - entry.lastUsed > IDLE_TIMEOUT_MS) {
+      if (now - entry.lastUsed > IDLE_TIMEOUT_MS && entry.checkedOut === 0) {
         closeOne(repoId);
       }
     }
@@ -69,7 +73,7 @@ function evictLRU(): void {
   let oldestId: string | null = null;
   let oldestTime = Infinity;
   for (const [id, entry] of pool) {
-    if (entry.lastUsed < oldestTime) {
+    if (entry.checkedOut === 0 && entry.lastUsed < oldestTime) {
       oldestTime = entry.lastUsed;
       oldestId = id;
     }
@@ -86,9 +90,9 @@ function closeOne(repoId: string): void {
   const entry = pool.get(repoId);
   if (!entry) return;
   for (const conn of entry.available) {
-    try { conn.close(); } catch {}
+    try { conn.close(); } catch (e) { console.error('GitNexus [pool:close-conn]:', e instanceof Error ? e.message : e); }
   }
-  try { entry.db.close(); } catch {}
+  try { entry.db.close(); } catch (e) { console.error('GitNexus [pool:close-db]:', e instanceof Error ? e.message : e); }
   pool.delete(repoId);
 }
 
@@ -96,16 +100,33 @@ function closeOne(repoId: string): void {
  * Create a new Connection from a repo's Database.
  * Silences stdout to prevent native module output from corrupting MCP stdio.
  */
+function silenceStdout(): void {
+  if (stdoutSilenceCount++ === 0) {
+    process.stdout.write = (() => true) as any;
+  }
+}
+
+function restoreStdout(): void {
+  if (--stdoutSilenceCount <= 0) {
+    stdoutSilenceCount = 0;
+    process.stdout.write = realStdoutWrite;
+  }
+}
+
 function createConnection(db: kuzu.Database): kuzu.Connection {
-  const origWrite = process.stdout.write;
+  silenceStdout();
-  process.stdout.write = (() => true) as any;
   try {
     return new kuzu.Connection(db);
   } finally {
-    process.stdout.write = origWrite;
+    restoreStdout();
   }
 }
 
+/** Query timeout in milliseconds */
+const QUERY_TIMEOUT_MS = 30_000;
+/** Waiter queue timeout in milliseconds */
+const WAITER_TIMEOUT_MS = 15_000;
+
 const LOCK_RETRY_ATTEMPTS = 3;
 const LOCK_RETRY_DELAY_MS = 2000;
 
@@ -134,8 +155,7 @@ export const initKuzu = async (repoId: string, dbPath: string): Promise<void> =>
   // avoids lock conflicts when `gitnexus analyze` is writing.
   let lastError: Error | null = null;
   for (let attempt = 1; attempt <= LOCK_RETRY_ATTEMPTS; attempt++) {
-    const origWrite = process.stdout.write;
+    silenceStdout();
-    process.stdout.write = (() => true) as any;
     try {
       const db = new kuzu.Database(
         dbPath,
@@ -143,7 +163,7 @@ export const initKuzu = async (repoId: string, dbPath: string): Promise<void> =>
         false, // enableCompression (default)
         true,  // readOnly
       );
-      process.stdout.write = origWrite;
+      restoreStdout();
 
       // Pre-create a small pool of connections
       const available: kuzu.Connection[] = [];
@@ -155,7 +175,7 @@ export const initKuzu = async (repoId: string, dbPath: string): Promise<void> =>
       ensureIdleTimer();
       return;
     } catch (err: any) {
-      process.stdout.write = origWrite;
+      restoreStdout();
       lastError = err instanceof Error ? err : new Error(String(err));
       const isLockError = lastError.message.includes('Could not set lock')
         || lastError.message.includes('lock');
@@ -189,10 +209,18 @@ function checkout(entry: PoolEntry): Promise<kuzu.Connection> {
     return Promise.resolve(createConnection(entry.db));
   }
 
-  // At capacity — queue the caller. checkin() will resolve this when
+  // At capacity — queue the caller with a timeout.
-  // a connection is returned, handing it directly to the next waiter.
+  return new Promise<kuzu.Connection>((resolve, reject) => {
-  return new Promise<kuzu.Connection>(resolve => {
+    const waiter = (conn: kuzu.Connection) => {
-    entry.waiters.push(resolve);
+      clearTimeout(timer);
+      resolve(conn);
+    };
+    const timer = setTimeout(() => {
+      const idx = entry.waiters.indexOf(waiter);
+      if (idx !== -1) entry.waiters.splice(idx, 1);
+      reject(new Error(`Connection pool exhausted: timed out after ${WAITER_TIMEOUT_MS}ms waiting for a free connection`));
+    }, WAITER_TIMEOUT_MS);
+    entry.waiters.push(waiter);
   });
 }
 
@@ -216,6 +244,15 @@ function checkin(entry: PoolEntry, conn: kuzu.Connection): void {
  * Execute a query on a specific repo's connection pool.
  * Automatically checks out a connection, runs the query, and returns it.
  */
+/** Race a promise against a timeout */
+function withTimeout<T>(promise: Promise<T>, ms: number, label: string): Promise<T> {
+  let timer: ReturnType<typeof setTimeout>;
+  const timeout = new Promise<never>((_, reject) => {
+    timer = setTimeout(() => reject(new Error(`${label} timed out after ${ms}ms`)), ms);
+  });
+  return Promise.race([promise, timeout]).finally(() => clearTimeout(timer));
+}
+
 export const executeQuery = async (repoId: string, cypher: string): Promise<any[]> => {
   const entry = pool.get(repoId);
   if (!entry) {
@@ -226,7 +263,39 @@ export const executeQuery = async (repoId: string, cypher: string): Promise<any[
 
   const conn = await checkout(entry);
   try {
-    const queryResult = await conn.query(cypher);
+    const queryResult = await withTimeout(conn.query(cypher), QUERY_TIMEOUT_MS, 'Query');
+    const result = Array.isArray(queryResult) ? queryResult[0] : queryResult;
+    const rows = await result.getAll();
+    return rows;
+  } finally {
+    checkin(entry, conn);
+  }
+};
+
+/**
+ * Execute a parameterized query on a specific repo's connection pool.
+ * Uses prepare/execute pattern to prevent Cypher injection.
+ */
+export const executeParameterized = async (
+  repoId: string,
+  cypher: string,
+  params: Record<string, any>,
+): Promise<any[]> => {
+  const entry = pool.get(repoId);
+  if (!entry) {
+    throw new Error(`KuzuDB not initialized for repo "${repoId}". Call initKuzu first.`);
+  }
+
+  entry.lastUsed = Date.now();
+
+  const conn = await checkout(entry);
+  try {
+    const stmt = await withTimeout(conn.prepare(cypher), QUERY_TIMEOUT_MS, 'Prepare');
+    if (!stmt.isSuccess()) {
+      const errMsg = await stmt.getErrorMessage();
+      throw new Error(`Prepare failed: ${errMsg}`);
+    }
+    const queryResult = await withTimeout(conn.execute(stmt, params), QUERY_TIMEOUT_MS, 'Execute');
     const result = Array.isArray(queryResult) ? queryResult[0] : queryResult;
     const rows = await result.getAll();
     return rows;

gitnexus/src/mcp/local/local-backend.ts

@@ -8,7 +8,7 @@
 
 import fs from 'fs/promises';
 import path from 'path';
-import { initKuzu, executeQuery, closeKuzu, isKuzuReady } from '../core/kuzu-adapter.js';
+import { initKuzu, executeQuery, executeParameterized, closeKuzu, isKuzuReady } from '../core/kuzu-adapter.js';
 // Embedding imports are lazy (dynamic import) to avoid loading onnxruntime-node
 // at MCP server startup — crashes on unsupported Node ABI versions (#89)
 // git utilities available if needed
@@ -24,7 +24,7 @@ import {
  * Quick test-file detection for filtering impact results.
  * Matches common test file patterns across all supported languages.
  */
-function isTestFilePath(filePath: string): boolean {
+export function isTestFilePath(filePath: string): boolean {
   const p = filePath.toLowerCase().replace(/\\/g, '/');
   return (
     p.includes('.test.') || p.includes('.spec.') ||
@@ -37,13 +37,30 @@ function isTestFilePath(filePath: string): boolean {
 }
 
 /** Valid KuzuDB node labels for safe Cypher query construction */
-const VALID_NODE_LABELS = new Set([
+export const VALID_NODE_LABELS = new Set([
   'File', 'Folder', 'Function', 'Class', 'Interface', 'Method', 'CodeElement',
   'Community', 'Process', 'Struct', 'Enum', 'Macro', 'Typedef', 'Union',
   'Namespace', 'Trait', 'Impl', 'TypeAlias', 'Const', 'Static', 'Property',
   'Record', 'Delegate', 'Annotation', 'Constructor', 'Template', 'Module',
 ]);
 
+/** Valid relation types for impact analysis filtering */
+export const VALID_RELATION_TYPES = new Set(['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS']);
+
+/** Regex to detect write operations in user-supplied Cypher queries */
+export const CYPHER_WRITE_RE = /\b(CREATE|DELETE|SET|MERGE|REMOVE|DROP|ALTER|COPY|DETACH)\b/i;
+
+/** Check if a Cypher query contains write operations */
+export function isWriteQuery(query: string): boolean {
+  return CYPHER_WRITE_RE.test(query);
+}
+
+/** Structured error logging for query failures — replaces empty catch blocks */
+function logQueryError(context: string, err: unknown): void {
+  const msg = err instanceof Error ? err.message : String(err);
+  console.error(`GitNexus [${context}]: ${msg}`);
+}
+
 export interface CodebaseContext {
   projectName: string;
   stats: {
@@ -387,46 +404,44 @@ export class LocalBackend {
         continue;
       }
       
-      const escaped = sym.nodeId.replace(/'/g, "''");
-      
       // Find processes this symbol participates in
       let processRows: any[] = [];
       try {
-        processRows = await executeQuery(repo.id, `
+        processRows = await executeParameterized(repo.id, `
-          MATCH (n {id: '${escaped}'})-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p:Process)
+          MATCH (n {id: $nodeId})-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p:Process)
           RETURN p.id AS pid, p.label AS label, p.heuristicLabel AS heuristicLabel, p.processType AS processType, p.stepCount AS stepCount, r.step AS step
-        `);
+        `, { nodeId: sym.nodeId });
-      } catch { /* symbol might not be in any process */ }
+      } catch (e) { logQueryError('query:process-lookup', e); }
-      
+
       // Get cluster membership + cohesion (cohesion used as internal ranking signal)
       let cohesion = 0;
       let module: string | undefined;
       try {
-        const cohesionRows = await executeQuery(repo.id, `
+        const cohesionRows = await executeParameterized(repo.id, `
-          MATCH (n {id: '${escaped}'})-[:CodeRelation {type: 'MEMBER_OF'}]->(c:Community)
+          MATCH (n {id: $nodeId})-[:CodeRelation {type: 'MEMBER_OF'}]->(c:Community)
           RETURN c.cohesion AS cohesion, c.heuristicLabel AS module
           LIMIT 1
-        `);
+        `, { nodeId: sym.nodeId });
         if (cohesionRows.length > 0) {
           cohesion = (cohesionRows[0].cohesion ?? cohesionRows[0][0]) || 0;
           module = cohesionRows[0].module ?? cohesionRows[0][1];
         }
-      } catch { /* no cluster info */ }
+      } catch (e) { logQueryError('query:cluster-info', e); }
-      
+
       // Optionally fetch content
       let content: string | undefined;
       if (includeContent) {
         try {
-          const contentRows = await executeQuery(repo.id, `
+          const contentRows = await executeParameterized(repo.id, `
-            MATCH (n {id: '${escaped}'})
+            MATCH (n {id: $nodeId})
             RETURN n.content AS content
-          `);
+          `, { nodeId: sym.nodeId });
           if (contentRows.length > 0) {
             content = contentRows[0].content ?? contentRows[0][0];
           }
-        } catch { /* skip */ }
+        } catch (e) { logQueryError('query:content-fetch', e); }
       }
-      
+
       const symbolEntry = {
         id: sym.nodeId,
         name: sym.name,
@@ -535,13 +550,12 @@ export class LocalBackend {
     for (const bm25Result of bm25Results) {
       const fullPath = bm25Result.filePath;
       try {
-        const symbolQuery = `
+        const symbols = await executeParameterized(repo.id, `
-          MATCH (n) 
+          MATCH (n)
-          WHERE n.filePath = '${fullPath.replace(/'/g, "''")}'
+          WHERE n.filePath = $filePath
           RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath, n.startLine AS startLine, n.endLine AS endLine
           LIMIT 3
-        `;
+        `, { filePath: fullPath });
-        const symbols = await executeQuery(repo.id, symbolQuery);
         
         if (symbols.length > 0) {
           for (const sym of symbols) {
@@ -619,12 +633,11 @@ export class LocalBackend {
         if (!VALID_NODE_LABELS.has(label)) continue;
         
         try {
-          const escapedId = nodeId.replace(/'/g, "''");
           const nodeQuery = label === 'File'
-            ? `MATCH (n:File {id: '${escapedId}'}) RETURN n.name AS name, n.filePath AS filePath`
+            ? `MATCH (n:File {id: $nodeId}) RETURN n.name AS name, n.filePath AS filePath`
-            : `MATCH (n:\`${label}\` {id: '${escapedId}'}) RETURN n.name AS name, n.filePath AS filePath, n.startLine AS startLine, n.endLine AS endLine`;
+            : `MATCH (n:\`${label}\` {id: $nodeId}) RETURN n.name AS name, n.filePath AS filePath, n.startLine AS startLine, n.endLine AS endLine`;
-          
+
-          const nodeRows = await executeQuery(repo.id, nodeQuery);
+          const nodeRows = await executeParameterized(repo.id, nodeQuery, { nodeId });
           if (nodeRows.length > 0) {
             const nodeRow = nodeRows[0];
             results.push({
@@ -659,6 +672,11 @@ export class LocalBackend {
       return { error: 'KuzuDB not ready. Index may be corrupted.' };
     }
 
+    // Block write operations (defense-in-depth — DB is already read-only)
+    if (CYPHER_WRITE_RE.test(params.query)) {
+      return { error: 'Write operations (CREATE, DELETE, SET, MERGE, REMOVE, DROP, ALTER, COPY, DETACH) are not allowed. The knowledge graph is read-only.' };
+    }
+
     try {
       const result = await executeQuery(repo.id, params.query);
       return result;
@@ -817,31 +835,32 @@ export class LocalBackend {
     let symbols: any[];
     
     if (uid) {
-      const escaped = uid.replace(/'/g, "''");
+      symbols = await executeParameterized(repo.id, `
-      symbols = await executeQuery(repo.id, `
+        MATCH (n {id: $uid})
-        MATCH (n {id: '${escaped}'})
         RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath, n.startLine AS startLine, n.endLine AS endLine${include_content ? ', n.content AS content' : ''}
         LIMIT 1
-      `);
+      `, { uid });
     } else {
-      const escaped = name!.replace(/'/g, "''");
       const isQualified = name!.includes('/') || name!.includes(':');
-      
+
       let whereClause: string;
+      let queryParams: Record<string, any>;
       if (file_path) {
-        const fpEscaped = file_path.replace(/'/g, "''");
+        whereClause = `WHERE n.name = $symName AND n.filePath CONTAINS $filePath`;
-        whereClause = `WHERE n.name = '${escaped}' AND n.filePath CONTAINS '${fpEscaped}'`;
+        queryParams = { symName: name!, filePath: file_path };
       } else if (isQualified) {
-        whereClause = `WHERE n.id = '${escaped}' OR n.name = '${escaped}'`;
+        whereClause = `WHERE n.id = $symName OR n.name = $symName`;
+        queryParams = { symName: name! };
       } else {
-        whereClause = `WHERE n.name = '${escaped}'`;
+        whereClause = `WHERE n.name = $symName`;
+        queryParams = { symName: name! };
       }
-      
+
-      symbols = await executeQuery(repo.id, `
+      symbols = await executeParameterized(repo.id, `
         MATCH (n) ${whereClause}
         RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath, n.startLine AS startLine, n.endLine AS endLine${include_content ? ', n.content AS content' : ''}
         LIMIT 10
-      `);
+      `, queryParams);
     }
     
     if (symbols.length === 0) {
@@ -865,32 +884,32 @@ export class LocalBackend {
     
     // Step 3: Build full context
     const sym = symbols[0];
-    const symId = (sym.id || sym[0]).replace(/'/g, "''");
+    const symId = sym.id || sym[0];
-    
+
     // Categorized incoming refs
-    const incomingRows = await executeQuery(repo.id, `
+    const incomingRows = await executeParameterized(repo.id, `
-      MATCH (caller)-[r:CodeRelation]->(n {id: '${symId}'})
+      MATCH (caller)-[r:CodeRelation]->(n {id: $symId})
       WHERE r.type IN ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS']
       RETURN r.type AS relType, caller.id AS uid, caller.name AS name, caller.filePath AS filePath, labels(caller)[0] AS kind
       LIMIT 30
-    `);
+    `, { symId });
-    
+
     // Categorized outgoing refs
-    const outgoingRows = await executeQuery(repo.id, `
+    const outgoingRows = await executeParameterized(repo.id, `
-      MATCH (n {id: '${symId}'})-[r:CodeRelation]->(target)
+      MATCH (n {id: $symId})-[r:CodeRelation]->(target)
       WHERE r.type IN ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS']
       RETURN r.type AS relType, target.id AS uid, target.name AS name, target.filePath AS filePath, labels(target)[0] AS kind
       LIMIT 30
-    `);
+    `, { symId });
-    
+
     // Process participation
     let processRows: any[] = [];
     try {
-      processRows = await executeQuery(repo.id, `
+      processRows = await executeParameterized(repo.id, `
-        MATCH (n {id: '${symId}'})-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p:Process)
+        MATCH (n {id: $symId})-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p:Process)
         RETURN p.id AS pid, p.heuristicLabel AS label, r.step AS step, p.stepCount AS stepCount
-      `);
+      `, { symId });
-    } catch { /* no process info */ }
+    } catch (e) { logQueryError('context:process-participation', e); }
     
     // Helper to categorize refs
     const categorize = (rows: any[]) => {
@@ -944,33 +963,31 @@ export class LocalBackend {
     }
     
     if (type === 'cluster') {
-      const escaped = name.replace(/'/g, "''");
+      const clusters = await executeParameterized(repo.id, `
-      const clusterQuery = `
         MATCH (c:Community)
-        WHERE c.label = '${escaped}' OR c.heuristicLabel = '${escaped}'
+        WHERE c.label = $clusterName OR c.heuristicLabel = $clusterName
         RETURN c.id AS id, c.label AS label, c.heuristicLabel AS heuristicLabel, c.cohesion AS cohesion, c.symbolCount AS symbolCount
-      `;
+      `, { clusterName: name });
-      const clusters = await executeQuery(repo.id, clusterQuery);
       if (clusters.length === 0) return { error: `Cluster '${name}' not found` };
-      
+
       const rawClusters = clusters.map((c: any) => ({
         id: c.id || c[0], label: c.label || c[1], heuristicLabel: c.heuristicLabel || c[2],
         cohesion: c.cohesion || c[3], symbolCount: c.symbolCount || c[4],
       }));
-      
+
       let totalSymbols = 0, weightedCohesion = 0;
       for (const c of rawClusters) {
         const s = c.symbolCount || 0;
         totalSymbols += s;
         weightedCohesion += (c.cohesion || 0) * s;
       }
-      
+
-      const members = await executeQuery(repo.id, `
+      const members = await executeParameterized(repo.id, `
         MATCH (n)-[:CodeRelation {type: 'MEMBER_OF'}]->(c:Community)
-        WHERE c.label = '${escaped}' OR c.heuristicLabel = '${escaped}'
+        WHERE c.label = $clusterName OR c.heuristicLabel = $clusterName
         RETURN DISTINCT n.name AS name, labels(n)[0] AS type, n.filePath AS filePath
         LIMIT 30
-      `);
+      `, { clusterName: name });
       
       return {
         cluster: {
@@ -988,21 +1005,21 @@ export class LocalBackend {
     }
     
     if (type === 'process') {
-      const processes = await executeQuery(repo.id, `
+      const processes = await executeParameterized(repo.id, `
         MATCH (p:Process)
-        WHERE p.label = '${name.replace(/'/g, "''")}' OR p.heuristicLabel = '${name.replace(/'/g, "''")}'
+        WHERE p.label = $processName OR p.heuristicLabel = $processName
         RETURN p.id AS id, p.label AS label, p.heuristicLabel AS heuristicLabel, p.processType AS processType, p.stepCount AS stepCount
         LIMIT 1
-      `);
+      `, { processName: name });
       if (processes.length === 0) return { error: `Process '${name}' not found` };
-      
+
       const proc = processes[0];
       const procId = proc.id || proc[0];
-      const steps = await executeQuery(repo.id, `
+      const steps = await executeParameterized(repo.id, `
-        MATCH (n)-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p {id: '${procId}'})
+        MATCH (n)-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p {id: $procId})
         RETURN n.name AS name, labels(n)[0] AS type, n.filePath AS filePath, r.step AS step
         ORDER BY r.step
-      `);
+      `, { procId });
       
       return {
         process: {
@@ -1069,13 +1086,13 @@ export class LocalBackend {
     // Map changed files to indexed symbols
     const changedSymbols: any[] = [];
     for (const file of changedFiles) {
-      const escaped = file.replace(/\\/g, '/').replace(/'/g, "''");
+      const normalizedFile = file.replace(/\\/g, '/');
       try {
-        const symbols = await executeQuery(repo.id, `
+        const symbols = await executeParameterized(repo.id, `
-          MATCH (n) WHERE n.filePath CONTAINS '${escaped}'
+          MATCH (n) WHERE n.filePath CONTAINS $filePath
           RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath
           LIMIT 20
-        `);
+        `, { filePath: normalizedFile });
         for (const sym of symbols) {
           changedSymbols.push({
             id: sym.id || sym[0],
@@ -1085,18 +1102,17 @@ export class LocalBackend {
             change_type: 'Modified',
           });
         }
-      } catch { /* skip */ }
+      } catch (e) { logQueryError('detect-changes:file-symbols', e); }
     }
-    
+
     // Find affected processes
     const affectedProcesses = new Map<string, any>();
     for (const sym of changedSymbols) {
-      const escaped = (sym.id as string).replace(/'/g, "''");
       try {
-        const procs = await executeQuery(repo.id, `
+        const procs = await executeParameterized(repo.id, `
-          MATCH (n {id: '${escaped}'})-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p:Process)
+          MATCH (n {id: $nodeId})-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p:Process)
           RETURN p.id AS pid, p.heuristicLabel AS label, p.processType AS processType, p.stepCount AS stepCount, r.step AS step
-        `);
+        `, { nodeId: sym.id });
         for (const proc of procs) {
           const pid = proc.pid || proc[0];
           if (!affectedProcesses.has(pid)) {
@@ -1113,9 +1129,9 @@ export class LocalBackend {
             step: proc.step || proc[4],
           });
         }
-      } catch { /* skip */ }
+      } catch (e) { logQueryError('detect-changes:process-lookup', e); }
     }
-    
+
     const processCount = affectedProcesses.size;
     const risk = processCount === 0 ? 'low' : processCount <= 5 ? 'medium' : processCount <= 15 ? 'high' : 'critical';
     
@@ -1147,10 +1163,19 @@ export class LocalBackend {
     
     const { new_name, file_path } = params;
     const dry_run = params.dry_run ?? true;
-    
+
     if (!params.symbol_name && !params.symbol_uid) {
       return { error: 'Either symbol_name or symbol_uid is required.' };
     }
+
+    /** Guard: ensure a file path resolves within the repo root (prevents path traversal) */
+    const assertSafePath = (filePath: string): string => {
+      const full = path.resolve(repo.repoPath, filePath);
+      if (!full.startsWith(repo.repoPath + path.sep) && full !== repo.repoPath) {
+        throw new Error(`Path traversal blocked: ${filePath}`);
+      }
+      return full;
+    };
     
     // Step 1: Find the target symbol (reuse context's lookup)
     const lookupResult = await this.context(repo, {
@@ -1186,15 +1211,16 @@ export class LocalBackend {
     // The definition itself
     if (sym.filePath && sym.startLine) {
       try {
-        const content = await fs.readFile(path.join(repo.repoPath, sym.filePath), 'utf-8');
+        const content = await fs.readFile(assertSafePath(sym.filePath), 'utf-8');
         const lines = content.split('\n');
         const lineIdx = sym.startLine - 1;
         if (lineIdx >= 0 && lineIdx < lines.length && lines[lineIdx].includes(oldName)) {
-          addEdit(sym.filePath, sym.startLine, lines[lineIdx].trim(), lines[lineIdx].replace(oldName, new_name).trim(), 'graph');
+          const defRegex = new RegExp(`\\b${oldName.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}\\b`, 'g');
+          addEdit(sym.filePath, sym.startLine, lines[lineIdx].trim(), lines[lineIdx].replace(defRegex, new_name).trim(), 'graph');
         }
-      } catch { /* skip */ }
+      } catch (e) { logQueryError('rename:read-definition', e); }
     }
-    
+
     // All incoming refs from graph (callers, importers, etc.)
     const allIncoming = [
       ...(lookupResult.incoming.calls || []),
@@ -1208,7 +1234,7 @@ export class LocalBackend {
     for (const ref of allIncoming) {
       if (!ref.filePath) continue;
       try {
-        const content = await fs.readFile(path.join(repo.repoPath, ref.filePath), 'utf-8');
+        const content = await fs.readFile(assertSafePath(ref.filePath), 'utf-8');
         const lines = content.split('\n');
         for (let i = 0; i < lines.length; i++) {
           if (lines[i].includes(oldName)) {
@@ -1217,9 +1243,9 @@ export class LocalBackend {
             break; // one edit per file from graph refs
           }
         }
-      } catch { /* skip */ }
+      } catch (e) { logQueryError('rename:read-ref', e); }
     }
-    
+
     // Step 3: Text search for refs the graph might have missed
     let astSearchEdits = 0;
     const graphFiles = new Set([sym.filePath, ...allIncoming.map(r => r.filePath)].filter(Boolean));
@@ -1229,7 +1255,7 @@ export class LocalBackend {
       const { execFileSync } = await import('child_process');
       const rgArgs = [
         '-l',
-        '--type-add', 'code:*.{ts,tsx,js,jsx,py,go,rs,java}',
+        '--type-add', 'code:*.{ts,tsx,js,jsx,py,go,rs,java,c,h,cpp,cc,cxx,hpp,hxx,hh,cs,php,swift}',
         '-t', 'code',
         `\\b${oldName}\\b`,
         '.',
@@ -1242,19 +1268,20 @@ export class LocalBackend {
         if (graphFiles.has(normalizedFile)) continue; // already covered by graph
         
         try {
-          const content = await fs.readFile(path.join(repo.repoPath, normalizedFile), 'utf-8');
+          const content = await fs.readFile(assertSafePath(normalizedFile), 'utf-8');
           const lines = content.split('\n');
           const regex = new RegExp(`\\b${oldName.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}\\b`, 'g');
           for (let i = 0; i < lines.length; i++) {
+            regex.lastIndex = 0;
             if (regex.test(lines[i])) {
+              regex.lastIndex = 0;
               addEdit(normalizedFile, i + 1, lines[i].trim(), lines[i].replace(regex, new_name).trim(), 'text_search');
               astSearchEdits++;
-              regex.lastIndex = 0; // reset regex
             }
           }
-        } catch { /* skip */ }
+        } catch (e) { logQueryError('rename:text-search-read', e); }
       }
-    } catch { /* rg not available or no additional matches */ }
+    } catch (e) { logQueryError('rename:ripgrep', e); }
     
     // Step 4: Apply or preview
     const allChanges = Array.from(changes.values());
@@ -1264,12 +1291,12 @@ export class LocalBackend {
       // Apply edits to files
       for (const change of allChanges) {
         try {
-          const fullPath = path.join(repo.repoPath, change.file_path);
+          const fullPath = assertSafePath(change.file_path);
           let content = await fs.readFile(fullPath, 'utf-8');
           const regex = new RegExp(`\\b${oldName.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}\\b`, 'g');
           content = content.replace(regex, new_name);
           await fs.writeFile(fullPath, content, 'utf-8');
-        } catch { /* skip failed files */ }
+        } catch (e) { logQueryError('rename:apply-edit', e); }
       }
     }
     
@@ -1298,22 +1325,22 @@ export class LocalBackend {
     
     const { target, direction } = params;
     const maxDepth = params.maxDepth || 3;
-    const relationTypes = params.relationTypes && params.relationTypes.length > 0
+    const rawRelTypes = params.relationTypes && params.relationTypes.length > 0
-      ? params.relationTypes
+      ? params.relationTypes.filter(t => VALID_RELATION_TYPES.has(t))
       : ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS'];
+    const relationTypes = rawRelTypes.length > 0 ? rawRelTypes : ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS'];
     const includeTests = params.includeTests ?? false;
     const minConfidence = params.minConfidence ?? 0;
-    
+
     const relTypeFilter = relationTypes.map(t => `'${t}'`).join(', ');
     const confidenceFilter = minConfidence > 0 ? ` AND r.confidence >= ${minConfidence}` : '';
-    
+
-    const targetQuery = `
+    const targets = await executeParameterized(repo.id, `
       MATCH (n)
-      WHERE n.name = '${target.replace(/'/g, "''")}'
+      WHERE n.name = $targetName
       RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath
       LIMIT 1
-    `;
+    `, { targetName: target });
-    const targets = await executeQuery(repo.id, targetQuery);
     if (targets.length === 0) return { error: `Target '${target}' not found` };
     
     const sym = targets[0];
@@ -1355,7 +1382,7 @@ export class LocalBackend {
             });
           }
         }
-      } catch { /* query failed for this depth level */ }
+      } catch (e) { logQueryError('impact:depth-traversal', e); }
       
       frontier = nextFrontier;
     }
@@ -1517,13 +1544,11 @@ export class LocalBackend {
     const repo = await this.resolveRepo(repoName);
     await this.ensureInitialized(repo.id);
 
-    const escaped = name.replace(/'/g, "''");
+    const clusters = await executeParameterized(repo.id, `
-    const clusterQuery = `
       MATCH (c:Community)
-      WHERE c.label = '${escaped}' OR c.heuristicLabel = '${escaped}'
+      WHERE c.label = $clusterName OR c.heuristicLabel = $clusterName
       RETURN c.id AS id, c.label AS label, c.heuristicLabel AS heuristicLabel, c.cohesion AS cohesion, c.symbolCount AS symbolCount
-    `;
+    `, { clusterName: name });
-    const clusters = await executeQuery(repo.id, clusterQuery);
     if (clusters.length === 0) return { error: `Cluster '${name}' not found` };
 
     const rawClusters = clusters.map((c: any) => ({
@@ -1538,12 +1563,12 @@ export class LocalBackend {
       weightedCohesion += (c.cohesion || 0) * s;
     }
 
-    const members = await executeQuery(repo.id, `
+    const members = await executeParameterized(repo.id, `
       MATCH (n)-[:CodeRelation {type: 'MEMBER_OF'}]->(c:Community)
-      WHERE c.label = '${escaped}' OR c.heuristicLabel = '${escaped}'
+      WHERE c.label = $clusterName OR c.heuristicLabel = $clusterName
       RETURN DISTINCT n.name AS name, labels(n)[0] AS type, n.filePath AS filePath
       LIMIT 30
-    `);
+    `, { clusterName: name });
 
     return {
       cluster: {
@@ -1568,22 +1593,21 @@ export class LocalBackend {
     const repo = await this.resolveRepo(repoName);
     await this.ensureInitialized(repo.id);
 
-    const escaped = name.replace(/'/g, "''");
+    const processes = await executeParameterized(repo.id, `
-    const processes = await executeQuery(repo.id, `
       MATCH (p:Process)
-      WHERE p.label = '${escaped}' OR p.heuristicLabel = '${escaped}'
+      WHERE p.label = $processName OR p.heuristicLabel = $processName
       RETURN p.id AS id, p.label AS label, p.heuristicLabel AS heuristicLabel, p.processType AS processType, p.stepCount AS stepCount
       LIMIT 1
-    `);
+    `, { processName: name });
     if (processes.length === 0) return { error: `Process '${name}' not found` };
 
     const proc = processes[0];
     const procId = proc.id || proc[0];
-    const steps = await executeQuery(repo.id, `
+    const steps = await executeParameterized(repo.id, `
-      MATCH (n)-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p {id: '${procId}'})
+      MATCH (n)-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p {id: $procId})
       RETURN n.name AS name, labels(n)[0] AS type, n.filePath AS filePath, r.step AS step
       ORDER BY r.step
-    `);
+    `, { procId });
 
     return {
       process: {

gitnexus/src/mcp/server.ts

@@ -11,6 +11,7 @@
  * Resources: repos, repo/{name}/context, repo/{name}/clusters, ...
  */
 
+import { createRequire } from 'module';
 import { Server } from '@modelcontextprotocol/sdk/server/index.js';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
 import {
@@ -80,10 +81,12 @@ function getNextStepHint(toolName: string, args: Record<string, any> | undefined
  * Transport-agnostic — caller connects the desired transport.
  */
 export function createMCPServer(backend: LocalBackend): Server {
+  const require = createRequire(import.meta.url);
+  const pkgVersion: string = require('../../package.json').version;
   const server = new Server(
     {
       name: 'gitnexus',
-      version: '1.1.9',
+      version: pkgVersion,
     },
     {
       capabilities: {
@@ -277,16 +280,22 @@ export async function startMCPServer(backend: LocalBackend): Promise<void> {
   const transport = new StdioServerTransport();
   await server.connect(transport);
 
-  // Handle graceful shutdown
+  // Graceful shutdown helper
-  process.on('SIGINT', async () => {
+  let shuttingDown = false;
-    await backend.disconnect();
+  const shutdown = async () => {
-    await server.close();
+    if (shuttingDown) return;
+    shuttingDown = true;
+    try { await backend.disconnect(); } catch {}
+    try { await server.close(); } catch {}
     process.exit(0);
-  });
+  };
 
-  process.on('SIGTERM', async () => {
+  // Handle graceful shutdown
-    await backend.disconnect();
+  process.on('SIGINT', shutdown);
-    await server.close();
+  process.on('SIGTERM', shutdown);
-    process.exit(0);
+
-  });
+  // Handle stdio errors — stdin close means the parent process is gone
+  process.stdin.on('end', shutdown);
+  process.stdin.on('error', () => shutdown());
+  process.stdout.on('error', () => shutdown());
 }

gitnexus/src/storage/git.ts

@@ -1,4 +1,5 @@
 import { execSync } from 'child_process';
+import path from 'path';
 
 // Git utilities for repository detection, commit tracking, and diff analysis
 
@@ -24,9 +25,11 @@ export const getCurrentCommit = (repoPath: string): string => {
  */
 export const getGitRoot = (fromPath: string): string | null => {
   try {
-    return execSync('git rev-parse --show-toplevel', { cwd: fromPath })
+    const raw = execSync('git rev-parse --show-toplevel', { cwd: fromPath })
       .toString()
       .trim();
+    // On Windows, git returns /d/Projects/Foo — path.resolve normalizes to D:\Projects\Foo
+    return path.resolve(raw);
   } catch {
     return null;
   }

gitnexus/src/storage/repo-manager.ts

@@ -201,9 +201,13 @@ export const registerRepo = async (repoPath: string, meta: RepoMeta): Promise<vo
   const { storagePath } = getStoragePaths(resolved);
 
   const entries = await readRegistry();
-  const existing = entries.findIndex(
+  const existing = entries.findIndex((e) => {
-    (e) => path.resolve(e.path) === resolved
+    const a = path.resolve(e.path);
-  );
+    const b = resolved;
+    return process.platform === 'win32'
+      ? a.toLowerCase() === b.toLowerCase()
+      : a === b;
+  });
 
   const entry: RegistryEntry = {
     name,
@@ -296,5 +300,10 @@ export const loadCLIConfig = async (): Promise<CLIConfig> => {
 export const saveCLIConfig = async (config: CLIConfig): Promise<void> => {
   const dir = getGlobalDir();
   await fs.mkdir(dir, { recursive: true });
-  await fs.writeFile(getGlobalConfigPath(), JSON.stringify(config, null, 2), 'utf-8');
+  const configPath = getGlobalConfigPath();
+  await fs.writeFile(configPath, JSON.stringify(config, null, 2), 'utf-8');
+  // Restrict file permissions on Unix (config may contain API keys)
+  if (process.platform !== 'win32') {
+    try { await fs.chmod(configPath, 0o600); } catch { /* best-effort */ }
+  }
 };

gitnexus/test/fixtures/mini-repo/src/db.ts

@@ -0,0 +1,19 @@
+import type { ValidationResult } from './validator';
+
+export interface DbRecord {
+  id: string;
+  value: string;
+  timestamp: number;
+}
+
+export async function saveToDb(input: ValidationResult): Promise<DbRecord> {
+  return {
+    id: Math.random().toString(36),
+    value: input.value,
+    timestamp: Date.now(),
+  };
+}
+
+export async function findById(id: string): Promise<DbRecord | null> {
+  return null;
+}

gitnexus/test/fixtures/mini-repo/src/formatter.ts

@@ -0,0 +1,15 @@
+import type { DbRecord } from './db';
+
+export function formatResponse(record: DbRecord): string {
+  return JSON.stringify({
+    success: true,
+    data: record,
+  });
+}
+
+export function formatError(message: string): string {
+  return JSON.stringify({
+    success: false,
+    error: message,
+  });
+}

gitnexus/test/fixtures/mini-repo/src/handler.ts

@@ -0,0 +1,15 @@
+import { validateInput } from './validator';
+import { saveToDb } from './db';
+import { formatResponse } from './formatter';
+
+export class RequestHandler {
+  async handleRequest(input: string): Promise<string> {
+    const validated = validateInput(input);
+    const saved = await saveToDb(validated);
+    return formatResponse(saved);
+  }
+}
+
+export function createHandler(): RequestHandler {
+  return new RequestHandler();
+}

gitnexus/test/fixtures/mini-repo/src/index.ts

@@ -0,0 +1,3 @@
+export { RequestHandler, createHandler } from './handler';
+export { validateInput, sanitize } from './validator';
+export { formatResponse, formatError } from './formatter';

gitnexus/test/fixtures/mini-repo/src/validator.ts

@@ -0,0 +1,15 @@
+export interface ValidationResult {
+  valid: boolean;
+  value: string;
+}
+
+export function validateInput(input: string): ValidationResult {
+  if (!input || input.trim().length === 0) {
+    return { valid: false, value: '' };
+  }
+  return { valid: true, value: input.trim() };
+}
+
+export function sanitize(input: string): string {
+  return input.replace(/[<>]/g, '');
+}

gitnexus/test/fixtures/sample-code/simple.c

@@ -0,0 +1,13 @@
+#include <stdio.h>
+
+int add(int a, int b) {
+    return a + b;
+}
+
+static int internal_helper(void) {
+    return 0;
+}
+
+void print_message(const char* msg) {
+    printf("%s\n", msg);
+}

gitnexus/test/fixtures/sample-code/simple.cpp

@@ -0,0 +1,19 @@
+#include <string>
+
+class UserManager {
+public:
+    void addUser(const std::string& name) {
+        users_.push_back(name);
+    }
+
+    int getCount() const {
+        return static_cast<int>(users_.size());
+    }
+
+private:
+    std::vector<std::string> users_;
+};
+
+int helperFunction(int x) {
+    return x * 2;
+}

gitnexus/test/fixtures/sample-code/simple.cs

@@ -0,0 +1,22 @@
+using System;
+
+namespace SampleApp
+{
+    public class Calculator
+    {
+        public int Add(int a, int b)
+        {
+            return a + b;
+        }
+
+        private int Multiply(int a, int b)
+        {
+            return a * b;
+        }
+    }
+
+    internal class Helper
+    {
+        public void DoWork() { }
+    }
+}

gitnexus/test/fixtures/sample-code/simple.go

@@ -0,0 +1,21 @@
+package main
+
+import "fmt"
+
+// ExportedFunction is a public function
+func ExportedFunction(name string) string {
+	return fmt.Sprintf("Hello, %s", name)
+}
+
+// unexportedFunction is a private function
+func unexportedFunction() int {
+	return 42
+}
+
+type UserService struct {
+	Name string
+}
+
+func (s *UserService) GetName() string {
+	return s.Name
+}

gitnexus/test/fixtures/sample-code/simple.java

@@ -0,0 +1,15 @@
+public class UserService {
+    private String name;
+
+    public UserService(String name) {
+        this.name = name;
+    }
+
+    public String getName() {
+        return this.name;
+    }
+
+    private void reset() {
+        this.name = "";
+    }
+}

gitnexus/test/fixtures/sample-code/simple.js

@@ -0,0 +1,32 @@
+const path = require('path');
+
+class EventEmitter {
+  constructor() {
+    this.listeners = {};
+  }
+
+  on(event, callback) {
+    if (!this.listeners[event]) {
+      this.listeners[event] = [];
+    }
+    this.listeners[event].push(callback);
+  }
+
+  emit(event, ...args) {
+    const handlers = this.listeners[event] || [];
+    handlers.forEach(handler => handler(...args));
+  }
+}
+
+function createLogger(prefix) {
+  return {
+    log: (msg) => console.log(`[${prefix}] ${msg}`),
+    error: (msg) => console.error(`[${prefix}] ${msg}`),
+  };
+}
+
+const formatDate = (date) => {
+  return date.toISOString().split('T')[0];
+};
+
+module.exports = { EventEmitter, createLogger, formatDate };

gitnexus/test/fixtures/sample-code/simple.php

@@ -0,0 +1,21 @@
+<?php
+
+function topLevelFunction(string $name): string {
+    return "Hello, " . $name;
+}
+
+class UserRepository {
+    private array $users = [];
+
+    public function addUser(string $name): void {
+        $this->users[] = $name;
+    }
+
+    private function validateName(string $name): bool {
+        return strlen($name) > 0;
+    }
+
+    public function getUsers(): array {
+        return $this->users;
+    }
+}

gitnexus/test/fixtures/sample-code/simple.py

@@ -0,0 +1,14 @@
+def public_function(x: int, y: int) -> int:
+    """A public function."""
+    return x + y
+
+def _private_helper(data: str) -> str:
+    """A private helper function."""
+    return data.strip()
+
+class Calculator:
+    def add(self, a: int, b: int) -> int:
+        return a + b
+
+    def _reset(self) -> None:
+        pass

gitnexus/test/fixtures/sample-code/simple.rs

@@ -0,0 +1,17 @@
+pub fn public_function(x: i32) -> i32 {
+    x + 1
+}
+
+fn private_function() -> &'static str {
+    "private"
+}
+
+pub struct Config {
+    pub name: String,
+}
+
+impl Config {
+    pub fn new(name: &str) -> Self {
+        Config { name: name.to_string() }
+    }
+}

gitnexus/test/fixtures/sample-code/simple.swift

@@ -0,0 +1,19 @@
+class UserManager {
+    var users: [String] = []
+
+    init() {
+        users = []
+    }
+
+    func addUser(_ name: String) {
+        users.append(name)
+    }
+
+    public func getCount() -> Int {
+        return users.count
+    }
+}
+
+func helperFunction() -> String {
+    return "swift helper"
+}

gitnexus/test/fixtures/sample-code/simple.ts

@@ -0,0 +1,27 @@
+export interface UserConfig {
+  name: string;
+  email: string;
+  active: boolean;
+}
+
+export function validateUser(config: UserConfig): boolean {
+  return config.name.length > 0 && config.email.includes('@');
+}
+
+export class UserService {
+  private users: UserConfig[] = [];
+
+  addUser(user: UserConfig): void {
+    if (validateUser(user)) {
+      this.users.push(user);
+    }
+  }
+
+  getUser(name: string): UserConfig | undefined {
+    return this.users.find(u => u.name === name);
+  }
+}
+
+function internalHelper(): string {
+  return 'helper';
+}

gitnexus/test/fixtures/sample-code/simple.tsx

@@ -0,0 +1,41 @@
+import React, { useState } from 'react';
+
+interface ButtonProps {
+  label: string;
+  onClick: () => void;
+}
+
+export class Counter extends React.Component<{}, { count: number }> {
+  state = { count: 0 };
+
+  increment() {
+    this.setState({ count: this.state.count + 1 });
+  }
+
+  render() {
+    return <button onClick={() => this.increment()}>{this.state.count}</button>;
+  }
+}
+
+export const Button: React.FC<ButtonProps> = ({ label, onClick }) => {
+  return <button onClick={onClick}>{label}</button>;
+};
+
+export function useCounter(initial: number = 0) {
+  const [count, setCount] = useState(initial);
+  const increment = () => setCount(c => c + 1);
+  const decrement = () => setCount(c => c - 1);
+  return { count, increment, decrement };
+}
+
+const App = () => {
+  const { count, increment } = useCounter();
+  return (
+    <div>
+      <h1>Count: {count}</h1>
+      <Button label="+" onClick={increment} />
+    </div>
+  );
+};
+
+export default App;

gitnexus/test/helpers/test-db.ts

@@ -0,0 +1,32 @@
+/**
+ * Test helper: Temporary KuzuDB factory
+ *
+ * Creates a temp directory, initializes KuzuDB with schema, and
+ * optionally loads minimal test data. Returns a cleanup function.
+ */
+import fs from 'fs/promises';
+import os from 'os';
+import path from 'path';
+
+export interface TestDBHandle {
+  dbPath: string;
+  cleanup: () => Promise<void>;
+}
+
+/**
+ * Create a temporary directory for KuzuDB tests.
+ * Returns the path and a cleanup function.
+ */
+export async function createTempDir(prefix: string = 'gitnexus-test-'): Promise<TestDBHandle> {
+  const tmpDir = await fs.mkdtemp(path.join(os.tmpdir(), prefix));
+  return {
+    dbPath: tmpDir,
+    cleanup: async () => {
+      try {
+        await fs.rm(tmpDir, { recursive: true, force: true });
+      } catch {
+        // best-effort cleanup
+      }
+    },
+  };
+}

gitnexus/test/helpers/test-graph.ts

@@ -0,0 +1,90 @@
+/**
+ * Test helper: In-memory knowledge graph builder
+ *
+ * Provides a convenient API for constructing test graphs
+ * without touching the filesystem or KuzuDB.
+ */
+import { createKnowledgeGraph } from '../../src/core/graph/graph.js';
+import type { KnowledgeGraph, GraphNode, NodeLabel, RelationshipType } from '../../src/core/graph/types.js';
+
+export interface TestNodeInput {
+  id: string;
+  label: NodeLabel;
+  name: string;
+  filePath: string;
+  startLine?: number;
+  endLine?: number;
+  isExported?: boolean;
+  extra?: Record<string, any>;
+}
+
+export interface TestRelInput {
+  sourceId: string;
+  targetId: string;
+  type: RelationshipType;
+  confidence?: number;
+  reason?: string;
+  step?: number;
+}
+
+/**
+ * Build a test graph from simple input arrays.
+ */
+export function buildTestGraph(
+  nodes: TestNodeInput[],
+  relationships: TestRelInput[] = [],
+): KnowledgeGraph {
+  const graph = createKnowledgeGraph();
+
+  for (const n of nodes) {
+    graph.addNode({
+      id: n.id,
+      label: n.label,
+      properties: {
+        name: n.name,
+        filePath: n.filePath,
+        startLine: n.startLine,
+        endLine: n.endLine,
+        isExported: n.isExported,
+        ...n.extra,
+      },
+    });
+  }
+
+  for (const r of relationships) {
+    graph.addRelationship({
+      id: `${r.sourceId}-${r.type}-${r.targetId}`,
+      sourceId: r.sourceId,
+      targetId: r.targetId,
+      type: r.type,
+      confidence: r.confidence ?? 1.0,
+      reason: r.reason ?? '',
+      step: r.step,
+    });
+  }
+
+  return graph;
+}
+
+/**
+ * Create a minimal graph with a few files, functions, and relationships.
+ * Useful as a baseline for integration tests.
+ */
+export function createMinimalTestGraph(): KnowledgeGraph {
+  return buildTestGraph(
+    [
+      { id: 'file:src/index.ts', label: 'File', name: 'index.ts', filePath: 'src/index.ts' },
+      { id: 'file:src/utils.ts', label: 'File', name: 'utils.ts', filePath: 'src/utils.ts' },
+      { id: 'func:main', label: 'Function', name: 'main', filePath: 'src/index.ts', startLine: 1, endLine: 10, isExported: true },
+      { id: 'func:helper', label: 'Function', name: 'helper', filePath: 'src/utils.ts', startLine: 1, endLine: 5, isExported: true },
+      { id: 'class:App', label: 'Class', name: 'App', filePath: 'src/index.ts', startLine: 12, endLine: 30, isExported: true },
+      { id: 'folder:src', label: 'Folder', name: 'src', filePath: 'src' },
+    ],
+    [
+      { sourceId: 'func:main', targetId: 'func:helper', type: 'CALLS' },
+      { sourceId: 'func:main', targetId: 'class:App', type: 'CALLS' },
+      { sourceId: 'file:src/index.ts', targetId: 'func:main', type: 'CONTAINS' },
+      { sourceId: 'file:src/utils.ts', targetId: 'func:helper', type: 'CONTAINS' },
+    ],
+  );
+}

gitnexus/test/integration/csv-pipeline.test.ts

@@ -0,0 +1,178 @@
+/**
+ * P1 Integration Tests: CSV Pipeline
+ *
+ * Tests: streamAllCSVsToDisk with real graph data.
+ * Covers hardening fixes: LRU cache (#24), BufferedCSVWriter flush
+ */
+import { describe, it, expect, beforeAll, afterAll } from 'vitest';
+import fs from 'fs/promises';
+import path from 'path';
+import { createTempDir, type TestDBHandle } from '../helpers/test-db.js';
+import { buildTestGraph } from '../helpers/test-graph.js';
+import { streamAllCSVsToDisk } from '../../src/core/kuzu/csv-generator.js';
+
+let tmpHandle: TestDBHandle;
+let csvDir: string;
+let repoDir: string;
+
+beforeAll(async () => {
+  tmpHandle = await createTempDir('csv-pipeline-test-');
+  csvDir = path.join(tmpHandle.dbPath, 'csv');
+  repoDir = path.join(tmpHandle.dbPath, 'repo');
+
+  // Create a fake repo directory with source files
+  await fs.mkdir(path.join(repoDir, 'src'), { recursive: true });
+  await fs.writeFile(
+    path.join(repoDir, 'src', 'index.ts'),
+    'export function main() {\n  console.log("hello");\n  helper();\n}\n\nexport class App {\n  run() {}\n}\n',
+  );
+  await fs.writeFile(
+    path.join(repoDir, 'src', 'utils.ts'),
+    'export function helper() {\n  return 42;\n}\n',
+  );
+});
+
+afterAll(async () => {
+  try { await tmpHandle.cleanup(); } catch { /* best-effort */ }
+});
+
+describe('streamAllCSVsToDisk', () => {
+  it('generates CSV files for all node types in the graph', async () => {
+    const graph = buildTestGraph(
+      [
+        { id: 'file:src/index.ts', label: 'File', name: 'index.ts', filePath: 'src/index.ts' },
+        { id: 'file:src/utils.ts', label: 'File', name: 'utils.ts', filePath: 'src/utils.ts' },
+        { id: 'func:main', label: 'Function', name: 'main', filePath: 'src/index.ts', startLine: 1, endLine: 4, isExported: true },
+        { id: 'func:helper', label: 'Function', name: 'helper', filePath: 'src/utils.ts', startLine: 1, endLine: 3, isExported: true },
+        { id: 'class:App', label: 'Class', name: 'App', filePath: 'src/index.ts', startLine: 6, endLine: 8, isExported: true },
+        { id: 'folder:src', label: 'Folder', name: 'src', filePath: 'src' },
+      ],
+      [
+        { sourceId: 'func:main', targetId: 'func:helper', type: 'CALLS' },
+        { sourceId: 'file:src/index.ts', targetId: 'func:main', type: 'CONTAINS' },
+        { sourceId: 'file:src/utils.ts', targetId: 'func:helper', type: 'CONTAINS' },
+      ],
+    );
+
+    const result = await streamAllCSVsToDisk(graph, repoDir, csvDir);
+
+    // Check that CSV files were created
+    expect(result.nodeFiles.size).toBeGreaterThan(0);
+    expect(result.relRows).toBe(3);
+
+    // Verify File CSV
+    const fileCsv = result.nodeFiles.get('File');
+    expect(fileCsv).toBeDefined();
+    expect(fileCsv!.rows).toBe(2);
+
+    // Verify Function CSV
+    const funcCsv = result.nodeFiles.get('Function');
+    expect(funcCsv).toBeDefined();
+    expect(funcCsv!.rows).toBe(2);
+
+    // Verify Class CSV
+    const classCsv = result.nodeFiles.get('Class');
+    expect(classCsv).toBeDefined();
+    expect(classCsv!.rows).toBe(1);
+
+    // Verify Folder CSV
+    const folderCsv = result.nodeFiles.get('Folder');
+    expect(folderCsv).toBeDefined();
+    expect(folderCsv!.rows).toBe(1);
+
+    // Verify relations CSV exists
+    const relContent = await fs.readFile(result.relCsvPath, 'utf-8');
+    const relLines = relContent.trim().split('\n');
+    expect(relLines.length).toBe(4); // header + 3 relationships
+  });
+
+  it('CSV content is properly escaped', async () => {
+    const graph = buildTestGraph([
+      {
+        id: 'file:src/index.ts',
+        label: 'File',
+        name: 'index.ts',
+        filePath: 'src/index.ts',
+      },
+    ]);
+
+    const result = await streamAllCSVsToDisk(graph, repoDir, csvDir);
+    const fileCsv = result.nodeFiles.get('File');
+    expect(fileCsv).toBeDefined();
+
+    const content = await fs.readFile(fileCsv!.csvPath, 'utf-8');
+    // Content should be properly quoted
+    expect(content).toContain('"file:src/index.ts"');
+    expect(content).toContain('"index.ts"');
+  });
+
+  it('handles community nodes with keywords', async () => {
+    const graph = buildTestGraph([
+      {
+        id: 'comm:auth',
+        label: 'Community' as any,
+        name: 'Auth',
+        filePath: '',
+        extra: {
+          heuristicLabel: 'Authentication',
+          keywords: ['auth', 'login', 'pass,word'],
+          description: 'Auth module',
+          enrichedBy: 'heuristic',
+          cohesion: 0.85,
+          symbolCount: 5,
+        },
+      },
+    ]);
+
+    const result = await streamAllCSVsToDisk(graph, repoDir, csvDir);
+    const commCsv = result.nodeFiles.get('Community');
+    expect(commCsv).toBeDefined();
+    expect(commCsv!.rows).toBe(1);
+
+    const content = await fs.readFile(commCsv!.csvPath, 'utf-8');
+    // Keywords with commas should be escaped with \,
+    expect(content).toContain('pass\\,word');
+  });
+
+  it('handles process nodes', async () => {
+    const graph = buildTestGraph([
+      {
+        id: 'proc:flow',
+        label: 'Process' as any,
+        name: 'LoginFlow',
+        filePath: '',
+        extra: {
+          heuristicLabel: 'User Login',
+          processType: 'intra_community',
+          stepCount: 3,
+          communities: ['auth'],
+          entryPointId: 'func:login',
+          terminalId: 'func:validate',
+        },
+      },
+    ]);
+
+    const result = await streamAllCSVsToDisk(graph, repoDir, csvDir);
+    const procCsv = result.nodeFiles.get('Process');
+    expect(procCsv).toBeDefined();
+    expect(procCsv!.rows).toBe(1);
+  });
+
+  it('deduplicates File nodes', async () => {
+    const graph = buildTestGraph([
+      { id: 'file:src/index.ts', label: 'File', name: 'index.ts', filePath: 'src/index.ts' },
+      // Duplicate (same id) — should not appear twice
+    ]);
+    // Add the same node again manually
+    graph.addNode({
+      id: 'file:src/index.ts',
+      label: 'File',
+      properties: { name: 'index.ts', filePath: 'src/index.ts' },
+    });
+
+    const result = await streamAllCSVsToDisk(graph, repoDir, csvDir);
+    const fileCsv = result.nodeFiles.get('File');
+    expect(fileCsv).toBeDefined();
+    expect(fileCsv!.rows).toBe(1);
+  });
+});

gitnexus/test/integration/filesystem-walker.test.ts

@@ -0,0 +1,92 @@
+import { describe, it, expect, beforeAll, afterAll } from 'vitest';
+import fs from 'fs/promises';
+import path from 'path';
+import os from 'os';
+import { walkRepositoryPaths, readFileContents } from '../../src/core/ingestion/filesystem-walker.js';
+
+describe('filesystem-walker', () => {
+  let tmpDir: string;
+
+  beforeAll(async () => {
+    tmpDir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-walker-test-'));
+
+    // Create test directory structure
+    await fs.mkdir(path.join(tmpDir, 'src'), { recursive: true });
+    await fs.mkdir(path.join(tmpDir, 'src', 'components'), { recursive: true });
+    await fs.mkdir(path.join(tmpDir, 'node_modules', 'lodash'), { recursive: true });
+    await fs.mkdir(path.join(tmpDir, '.git'), { recursive: true });
+
+    await fs.writeFile(path.join(tmpDir, 'src', 'index.ts'), 'export const main = () => {}');
+    await fs.writeFile(path.join(tmpDir, 'src', 'utils.ts'), 'export const helper = () => {}');
+    await fs.writeFile(path.join(tmpDir, 'src', 'components', 'Button.tsx'), 'export const Button = () => <div/>');
+    await fs.writeFile(path.join(tmpDir, 'node_modules', 'lodash', 'index.js'), 'module.exports = {}');
+    await fs.writeFile(path.join(tmpDir, '.git', 'HEAD'), 'ref: refs/heads/main');
+    await fs.writeFile(path.join(tmpDir, 'package.json'), '{}');
+    await fs.writeFile(path.join(tmpDir, 'src', 'image.png'), Buffer.from([0x89, 0x50, 0x4E, 0x47]));
+  });
+
+  afterAll(async () => {
+    try {
+      await fs.rm(tmpDir, { recursive: true, force: true });
+    } catch { /* best-effort */ }
+  });
+
+  describe('walkRepositoryPaths', () => {
+    it('discovers source files', async () => {
+      const files = await walkRepositoryPaths(tmpDir);
+      const paths = files.map(f => f.path.replace(/\\/g, '/'));
+      expect(paths.some(p => p.includes('src/index.ts'))).toBe(true);
+      expect(paths.some(p => p.includes('src/utils.ts'))).toBe(true);
+    });
+
+    it('discovers nested files', async () => {
+      const files = await walkRepositoryPaths(tmpDir);
+      const paths = files.map(f => f.path.replace(/\\/g, '/'));
+      expect(paths.some(p => p.includes('components/Button.tsx'))).toBe(true);
+    });
+
+    it('skips node_modules', async () => {
+      const files = await walkRepositoryPaths(tmpDir);
+      const paths = files.map(f => f.path.replace(/\\/g, '/'));
+      expect(paths.every(p => !p.includes('node_modules'))).toBe(true);
+    });
+
+    it('skips .git directory', async () => {
+      const files = await walkRepositoryPaths(tmpDir);
+      const paths = files.map(f => f.path.replace(/\\/g, '/'));
+      expect(paths.every(p => !p.includes('.git/'))).toBe(true);
+    });
+
+    it('returns file sizes', async () => {
+      const files = await walkRepositoryPaths(tmpDir);
+      for (const file of files) {
+        expect(typeof file.size).toBe('number');
+        expect(file.size).toBeGreaterThan(0);
+      }
+    });
+
+    it('calls progress callback', async () => {
+      const onProgress = vi.fn();
+      await walkRepositoryPaths(tmpDir, onProgress);
+      expect(onProgress).toHaveBeenCalled();
+    });
+  });
+
+  describe('readFileContents', () => {
+    it('reads file contents by relative paths', async () => {
+      const contents = await readFileContents(tmpDir, ['src/index.ts', 'src/utils.ts']);
+      expect(contents.get('src/index.ts')).toContain('main');
+      expect(contents.get('src/utils.ts')).toContain('helper');
+    });
+
+    it('handles empty path list', async () => {
+      const contents = await readFileContents(tmpDir, []);
+      expect(contents.size).toBe(0);
+    });
+
+    it('skips non-existent files gracefully', async () => {
+      const contents = await readFileContents(tmpDir, ['nonexistent.ts']);
+      expect(contents.size).toBe(0);
+    });
+  });
+});

gitnexus/test/integration/kuzu-pool.test.ts

@@ -0,0 +1,179 @@
+/**
+ * P0 Integration Tests: KuzuDB Connection Pool
+ *
+ * Tests: initKuzu, executeQuery, executeParameterized, closeKuzu lifecycle
+ * Covers hardening fixes: parameterized queries, query timeout,
+ * waiter queue timeout, idle eviction guards, stdout silencing race
+ */
+import { describe, it, expect, beforeAll, afterAll, afterEach } from 'vitest';
+import fs from 'fs/promises';
+import path from 'path';
+import kuzu from 'kuzu';
+import { createTempDir, type TestDBHandle } from '../helpers/test-db.js';
+import {
+  initKuzu,
+  executeQuery,
+  executeParameterized,
+  closeKuzu,
+  isKuzuReady,
+} from '../../src/mcp/core/kuzu-adapter.js';
+import { NODE_SCHEMA_QUERIES, REL_SCHEMA_QUERIES } from '../../src/core/kuzu/schema.js';
+
+let tmpHandle: TestDBHandle;
+let dbPath: string;
+const REPO_ID = 'test-repo';
+
+/**
+ * Create a writable KuzuDB with schema and seed data.
+ * The pool opens it read-only, so we must create it separately.
+ */
+async function createTestDB(dbDir: string): Promise<void> {
+  const db = new kuzu.Database(dbDir);
+  const conn = new kuzu.Connection(db);
+
+  // Create schema
+  for (const q of NODE_SCHEMA_QUERIES) {
+    await conn.query(q);
+  }
+  for (const q of REL_SCHEMA_QUERIES) {
+    await conn.query(q);
+  }
+
+  // Insert test data
+  await conn.query(`CREATE (f:File {id: 'file:index.ts', name: 'index.ts', filePath: 'src/index.ts', content: ''})`);
+  await conn.query(`CREATE (fn:Function {id: 'func:main', name: 'main', filePath: 'src/index.ts', startLine: 1, endLine: 10, isExported: true, content: '', description: ''})`);
+  await conn.query(`CREATE (fn2:Function {id: 'func:helper', name: 'helper', filePath: 'src/utils.ts', startLine: 1, endLine: 5, isExported: true, content: '', description: ''})`);
+  await conn.query(`
+    MATCH (a:Function), (b:Function)
+    WHERE a.id = 'func:main' AND b.id = 'func:helper'
+    CREATE (a)-[:CodeRelation {type: 'CALLS', confidence: 1.0, reason: 'direct', step: 0}]->(b)
+  `);
+
+  conn.close();
+  db.close();
+}
+
+beforeAll(async () => {
+  tmpHandle = await createTempDir('kuzu-pool-test-');
+  dbPath = path.join(tmpHandle.dbPath, 'kuzu');
+  // KuzuDB creates the directory itself — do NOT mkdir
+  await createTestDB(dbPath);
+}, 30000);
+
+afterAll(async () => {
+  // NOTE: We intentionally skip closeKuzu() here because KuzuDB native
+  // cleanup in forked workers can cause segfaults on process exit.
+  // The OS reclaims resources when the worker process terminates.
+  try { await tmpHandle.cleanup(); } catch { /* best-effort */ }
+});
+
+afterEach(async () => {
+  // Clean up specific repo IDs used in tests, not all
+  try { await closeKuzu(REPO_ID); } catch { /* best-effort */ }
+  try { await closeKuzu('repo1'); } catch { /* best-effort */ }
+  try { await closeKuzu('repo2'); } catch { /* best-effort */ }
+});
+
+// ─── Lifecycle: init → query → close ─────────────────────────────────
+
+describe('pool lifecycle', () => {
+  it('initKuzu + executeQuery + closeKuzu', async () => {
+    await initKuzu(REPO_ID, dbPath);
+    expect(isKuzuReady(REPO_ID)).toBe(true);
+
+    const rows = await executeQuery(REPO_ID, 'MATCH (n:Function) RETURN n.name AS name');
+    expect(rows.length).toBeGreaterThanOrEqual(2);
+    const names = rows.map((r: any) => r.name);
+    expect(names).toContain('main');
+    expect(names).toContain('helper');
+
+    await closeKuzu(REPO_ID);
+    expect(isKuzuReady(REPO_ID)).toBe(false);
+  });
+
+  it('initKuzu reuses existing pool entry', async () => {
+    await initKuzu(REPO_ID, dbPath);
+    await initKuzu(REPO_ID, dbPath); // second call should be no-op
+    expect(isKuzuReady(REPO_ID)).toBe(true);
+  });
+
+  it('closeKuzu is idempotent', async () => {
+    await initKuzu(REPO_ID, dbPath);
+    await closeKuzu(REPO_ID);
+    await closeKuzu(REPO_ID); // second close should not throw
+    expect(isKuzuReady(REPO_ID)).toBe(false);
+  });
+
+  it('closeKuzu with no args closes all repos', async () => {
+    await initKuzu('repo1', dbPath);
+    await initKuzu('repo2', dbPath);
+    expect(isKuzuReady('repo1')).toBe(true);
+    expect(isKuzuReady('repo2')).toBe(true);
+
+    await closeKuzu();
+    expect(isKuzuReady('repo1')).toBe(false);
+    expect(isKuzuReady('repo2')).toBe(false);
+  });
+});
+
+// ─── Parameterized queries ───────────────────────────────────────────
+
+describe('executeParameterized', () => {
+  it('works with parameterized query', async () => {
+    await initKuzu(REPO_ID, dbPath);
+    const rows = await executeParameterized(
+      REPO_ID,
+      'MATCH (n:Function) WHERE n.name = $name RETURN n.name AS name',
+      { name: 'main' },
+    );
+    expect(rows).toHaveLength(1);
+    expect(rows[0].name).toBe('main');
+  });
+
+  it('injection attempt is harmless with parameterized query', async () => {
+    await initKuzu(REPO_ID, dbPath);
+    const rows = await executeParameterized(
+      REPO_ID,
+      'MATCH (n:Function) WHERE n.name = $name RETURN n.name AS name',
+      { name: "' OR 1=1 --" }, // SQL/Cypher injection attempt
+    );
+    // Should return 0 rows, not all rows
+    expect(rows).toHaveLength(0);
+  });
+});
+
+// ─── Error handling ──────────────────────────────────────────────────
+
+describe('error handling', () => {
+  it('throws when querying uninitialized repo', async () => {
+    await expect(executeQuery('nonexistent-repo', 'MATCH (n) RETURN n'))
+      .rejects.toThrow(/not initialized/);
+  });
+
+  it('throws when db path does not exist', async () => {
+    await expect(initKuzu('bad-repo', '/nonexistent/path/kuzu'))
+      .rejects.toThrow();
+  });
+
+  it('read-only mode: write query throws', async () => {
+    await initKuzu(REPO_ID, dbPath);
+    await expect(executeQuery(REPO_ID, "CREATE (n:Function {id: 'new', name: 'new', filePath: '', startLine: 0, endLine: 0, isExported: false, content: '', description: ''})"))
+      .rejects.toThrow();
+  });
+});
+
+// ─── Relationship queries ────────────────────────────────────────────
+
+describe('relationship queries', () => {
+  it('can query relationships', async () => {
+    await initKuzu(REPO_ID, dbPath);
+    const rows = await executeQuery(
+      REPO_ID,
+      `MATCH (a:Function)-[r:CodeRelation {type: 'CALLS'}]->(b:Function) RETURN a.name AS caller, b.name AS callee`,
+    );
+    expect(rows.length).toBeGreaterThanOrEqual(1);
+    const row = rows.find((r: any) => r.caller === 'main');
+    expect(row).toBeDefined();
+    expect(row.callee).toBe('helper');
+  });
+});

gitnexus/test/integration/local-backend.test.ts

@@ -0,0 +1,254 @@
+/**
+ * P0 Integration Tests: Local Backend
+ *
+ * Tests tool implementations via direct KuzuDB queries.
+ * The full LocalBackend.callTool() requires a global registry,
+ * so here we test the security-critical behaviors directly:
+ * - Write-operation blocking in cypher
+ * - Query execution via the pool
+ * - Parameterized queries preventing injection
+ * - Read-only enforcement
+ *
+ * Covers hardening fixes: #1 (parameterized queries), #2 (write blocking),
+ * #3 (path traversal), #4 (relation allowlist), #25 (regex lastIndex),
+ * #26 (rename first-occurrence-only)
+ */
+import { describe, it, expect, beforeAll, afterAll } from 'vitest';
+import fs from 'fs/promises';
+import path from 'path';
+import kuzu from 'kuzu';
+import { createTempDir, type TestDBHandle } from '../helpers/test-db.js';
+import {
+  initKuzu,
+  executeQuery,
+  executeParameterized,
+  closeKuzu,
+} from '../../src/mcp/core/kuzu-adapter.js';
+import { NODE_SCHEMA_QUERIES, REL_SCHEMA_QUERIES } from '../../src/core/kuzu/schema.js';
+import {
+  CYPHER_WRITE_RE,
+  VALID_RELATION_TYPES,
+  isWriteQuery,
+} from '../../src/mcp/local/local-backend.js';
+
+let tmpHandle: TestDBHandle;
+let dbPath: string;
+const REPO_ID = 'backend-test';
+
+async function createTestDB(dbDir: string): Promise<void> {
+  const db = new kuzu.Database(dbDir);
+  const conn = new kuzu.Connection(db);
+
+  for (const q of NODE_SCHEMA_QUERIES) {
+    await conn.query(q);
+  }
+  for (const q of REL_SCHEMA_QUERIES) {
+    await conn.query(q);
+  }
+
+  // Insert test data: files, functions, classes, relationships
+  await conn.query(`CREATE (f:File {id: 'file:auth.ts', name: 'auth.ts', filePath: 'src/auth.ts', content: 'auth module'})`);
+  await conn.query(`CREATE (f:File {id: 'file:utils.ts', name: 'utils.ts', filePath: 'src/utils.ts', content: 'utils module'})`);
+  await conn.query(`CREATE (fn:Function {id: 'func:login', name: 'login', filePath: 'src/auth.ts', startLine: 1, endLine: 15, isExported: true, content: 'function login() {}', description: 'User login'})`);
+  await conn.query(`CREATE (fn:Function {id: 'func:validate', name: 'validate', filePath: 'src/auth.ts', startLine: 17, endLine: 25, isExported: true, content: 'function validate() {}', description: 'Validate input'})`);
+  await conn.query(`CREATE (fn:Function {id: 'func:hash', name: 'hash', filePath: 'src/utils.ts', startLine: 1, endLine: 8, isExported: true, content: 'function hash() {}', description: 'Hash utility'})`);
+  await conn.query(`CREATE (c:Class {id: 'class:AuthService', name: 'AuthService', filePath: 'src/auth.ts', startLine: 30, endLine: 60, isExported: true, content: 'class AuthService {}', description: 'Authentication service'})`);
+  await conn.query(`CREATE (c:Community {id: 'comm:auth', label: 'Auth', heuristicLabel: 'Authentication', keywords: ['auth', 'login'], description: 'Auth module', enrichedBy: 'heuristic', cohesion: 0.8, symbolCount: 3})`);
+  await conn.query(`CREATE (p:Process {id: 'proc:login-flow', label: 'LoginFlow', heuristicLabel: 'User Login', processType: 'intra_community', stepCount: 2, communities: ['auth'], entryPointId: 'func:login', terminalId: 'func:validate'})`);
+
+  // Relationships
+  await conn.query(`
+    MATCH (a:Function), (b:Function) WHERE a.id = 'func:login' AND b.id = 'func:validate'
+    CREATE (a)-[:CodeRelation {type: 'CALLS', confidence: 1.0, reason: 'direct', step: 0}]->(b)
+  `);
+  await conn.query(`
+    MATCH (a:Function), (b:Function) WHERE a.id = 'func:login' AND b.id = 'func:hash'
+    CREATE (a)-[:CodeRelation {type: 'CALLS', confidence: 0.9, reason: 'import-resolved', step: 0}]->(b)
+  `);
+  await conn.query(`
+    MATCH (a:Function), (c:Community) WHERE a.id = 'func:login' AND c.id = 'comm:auth'
+    CREATE (a)-[:CodeRelation {type: 'MEMBER_OF', confidence: 1.0, reason: '', step: 0}]->(c)
+  `);
+  await conn.query(`
+    MATCH (a:Function), (p:Process) WHERE a.id = 'func:login' AND p.id = 'proc:login-flow'
+    CREATE (a)-[:CodeRelation {type: 'STEP_IN_PROCESS', confidence: 1.0, reason: '', step: 1}]->(p)
+  `);
+  await conn.query(`
+    MATCH (a:Function), (p:Process) WHERE a.id = 'func:validate' AND p.id = 'proc:login-flow'
+    CREATE (a)-[:CodeRelation {type: 'STEP_IN_PROCESS', confidence: 1.0, reason: '', step: 2}]->(p)
+  `);
+
+  conn.close();
+  db.close();
+}
+
+beforeAll(async () => {
+  tmpHandle = await createTempDir('backend-test-');
+  dbPath = path.join(tmpHandle.dbPath, 'kuzu');
+  // KuzuDB creates the directory itself — do NOT mkdir
+  await createTestDB(dbPath);
+  await initKuzu(REPO_ID, dbPath);
+}, 30000);
+
+afterAll(async () => {
+  // NOTE: We intentionally skip closeKuzu() here because KuzuDB native
+  // cleanup in forked workers can cause segfaults on process exit.
+  // The OS reclaims resources when the worker process terminates.
+  try { await tmpHandle.cleanup(); } catch { /* best-effort */ }
+});
+
+// ─── Cypher write blocking ───────────────────────────────────────────
+
+describe('cypher write blocking', () => {
+  const allWriteKeywords = ['CREATE', 'DELETE', 'SET', 'MERGE', 'REMOVE', 'DROP', 'ALTER', 'COPY', 'DETACH'];
+
+  for (const keyword of allWriteKeywords) {
+    it(`blocks ${keyword} query`, () => {
+      const blocked = isWriteQuery(`MATCH (n) ${keyword} n.name = "x"`);
+      expect(blocked).toBe(true);
+    });
+  }
+
+  it('allows valid read queries through the pool', async () => {
+    const rows = await executeQuery(REPO_ID, 'MATCH (n:Function) RETURN n.name AS name ORDER BY n.name');
+    expect(rows.length).toBeGreaterThanOrEqual(3);
+  });
+});
+
+// ─── Parameterized queries ───────────────────────────────────────────
+
+describe('parameterized queries', () => {
+  it('finds exact match with parameter', async () => {
+    const rows = await executeParameterized(
+      REPO_ID,
+      'MATCH (n:Function) WHERE n.name = $name RETURN n.name AS name, n.filePath AS filePath',
+      { name: 'login' },
+    );
+    expect(rows).toHaveLength(1);
+    expect(rows[0].name).toBe('login');
+    expect(rows[0].filePath).toBe('src/auth.ts');
+  });
+
+  it('injection is harmless', async () => {
+    const rows = await executeParameterized(
+      REPO_ID,
+      'MATCH (n:Function) WHERE n.name = $name RETURN n.name AS name',
+      { name: "login' OR '1'='1" },
+    );
+    expect(rows).toHaveLength(0);
+  });
+});
+
+// ─── Relation type filtering ─────────────────────────────────────────
+
+describe('relation type filtering', () => {
+  it('only allows valid relation types in queries', () => {
+    const validTypes = ['CALLS', 'IMPORTS', 'EXTENDS', 'IMPLEMENTS'];
+    const invalidTypes = ['CONTAINS', 'STEP_IN_PROCESS', 'MEMBER_OF', 'DROP_TABLE'];
+
+    for (const t of validTypes) {
+      expect(VALID_RELATION_TYPES.has(t)).toBe(true);
+    }
+    for (const t of invalidTypes) {
+      expect(VALID_RELATION_TYPES.has(t)).toBe(false);
+    }
+  });
+
+  it('can query relationships with valid types', async () => {
+    const rows = await executeQuery(
+      REPO_ID,
+      `MATCH (a:Function)-[r:CodeRelation {type: 'CALLS'}]->(b:Function) RETURN a.name AS caller, b.name AS callee ORDER BY b.name`,
+    );
+    expect(rows.length).toBeGreaterThanOrEqual(2);
+  });
+});
+
+// ─── Process queries ─────────────────────────────────────────────────
+
+describe('process queries', () => {
+  it('can find processes', async () => {
+    const rows = await executeQuery(REPO_ID, 'MATCH (p:Process) RETURN p.heuristicLabel AS label, p.stepCount AS steps');
+    expect(rows.length).toBeGreaterThanOrEqual(1);
+    expect(rows[0].label).toBe('User Login');
+  });
+
+  it('can trace process steps', async () => {
+    const rows = await executeQuery(
+      REPO_ID,
+      `MATCH (s)-[r:CodeRelation {type: 'STEP_IN_PROCESS'}]->(p:Process)
+       WHERE p.id = 'proc:login-flow'
+       RETURN s.name AS symbol, r.step AS step
+       ORDER BY r.step`,
+    );
+    expect(rows).toHaveLength(2);
+    expect(rows[0].symbol).toBe('login');
+    expect(rows[0].step).toBe(1);
+    expect(rows[1].symbol).toBe('validate');
+    expect(rows[1].step).toBe(2);
+  });
+});
+
+// ─── Community queries ───────────────────────────────────────────────
+
+describe('community queries', () => {
+  it('can find communities', async () => {
+    const rows = await executeQuery(REPO_ID, 'MATCH (c:Community) RETURN c.heuristicLabel AS label');
+    expect(rows.length).toBeGreaterThanOrEqual(1);
+    expect(rows[0].label).toBe('Authentication');
+  });
+
+  it('can find community members', async () => {
+    const rows = await executeQuery(
+      REPO_ID,
+      `MATCH (f)-[:CodeRelation {type: 'MEMBER_OF'}]->(c:Community)
+       WHERE c.heuristicLabel = 'Authentication'
+       RETURN f.name AS name`,
+    );
+    expect(rows.length).toBeGreaterThanOrEqual(1);
+    expect(rows[0].name).toBe('login');
+  });
+});
+
+// ─── Read-only enforcement ───────────────────────────────────────────
+
+describe('read-only database', () => {
+  it('rejects write operations at DB level', async () => {
+    await expect(
+      executeQuery(REPO_ID, `CREATE (n:Function {id: 'new', name: 'new', filePath: '', startLine: 0, endLine: 0, isExported: false, content: '', description: ''})`)
+    ).rejects.toThrow();
+  });
+});
+
+// ─── Regex lastIndex hardening (#25) ─────────────────────────────────
+
+describe('regex lastIndex (hardening #25)', () => {
+  it('CYPHER_WRITE_RE is non-global (no sticky lastIndex)', () => {
+    expect(CYPHER_WRITE_RE.global).toBe(false);
+    expect(CYPHER_WRITE_RE.sticky).toBe(false);
+  });
+
+  it('works correctly across multiple consecutive calls', () => {
+    // If the regex were global, lastIndex could cause false results
+    const results = [
+      isWriteQuery('CREATE (n)'),     // true
+      isWriteQuery('MATCH (n) RETURN n'), // false
+      isWriteQuery('DELETE n'),       // true
+      isWriteQuery('MATCH (n) RETURN n'), // false
+      isWriteQuery('SET n.x = 1'),    // true
+    ];
+    expect(results).toEqual([true, false, true, false, true]);
+  });
+});
+
+// ─── Content queries (include_content equivalent) ────────────────────
+
+describe('content queries', () => {
+  it('can retrieve symbol content', async () => {
+    const rows = await executeQuery(
+      REPO_ID,
+      `MATCH (n:Function) WHERE n.name = 'login' RETURN n.content AS content`,
+    );
+    expect(rows).toHaveLength(1);
+    expect(rows[0].content).toContain('function login');
+  });
+});

gitnexus/test/integration/parsing.test.ts

@@ -0,0 +1,211 @@
+/**
+ * P1 Integration Tests: Tree-sitter Parsing
+ *
+ * Tests parsing of sample files via tree-sitter.
+ * Covers hardening fixes: Swift init constructor (#18),
+ * PHP export detection (#20), symbol ID with startLine (#19),
+ * definition node range (#22).
+ */
+import { describe, it, expect, beforeAll } from 'vitest';
+import fs from 'fs/promises';
+import path from 'path';
+import { createKnowledgeGraph } from '../../src/core/graph/graph.js';
+import { isNodeExported } from '../../src/core/ingestion/parsing-processor.js';
+
+const FIXTURES_DIR = path.join(process.cwd(), 'test', 'fixtures', 'sample-code');
+
+// We test isNodeExported directly since it's a pure function
+// that only needs a mock AST node, name, and language string.
+
+/**
+ * Minimal mock of a tree-sitter AST node.
+ */
+function mockNode(type: string, text: string = '', parent?: any): any {
+  return {
+    type,
+    text,
+    parent: parent || null,
+    childCount: 0,
+    child: () => null,
+  };
+}
+
+// ─── isNodeExported per-language ─────────────────────────────────────
+
+describe('isNodeExported', () => {
+  // TypeScript/JavaScript
+  describe('typescript', () => {
+    it('returns true when ancestor is export_statement', () => {
+      const exportStmt = mockNode('export_statement', 'export function foo() {}');
+      const fnDecl = mockNode('function_declaration', 'function foo() {}', exportStmt);
+      const nameNode = mockNode('identifier', 'foo', fnDecl);
+      expect(isNodeExported(nameNode, 'foo', 'typescript')).toBe(true);
+    });
+
+    it('returns false for non-exported function', () => {
+      const fnDecl = mockNode('function_declaration', 'function foo() {}');
+      const nameNode = mockNode('identifier', 'foo', fnDecl);
+      expect(isNodeExported(nameNode, 'foo', 'typescript')).toBe(false);
+    });
+
+    it('returns true when text starts with "export "', () => {
+      const parent = mockNode('lexical_declaration', 'export const foo = 1');
+      const nameNode = mockNode('identifier', 'foo', parent);
+      expect(isNodeExported(nameNode, 'foo', 'typescript')).toBe(true);
+    });
+  });
+
+  // Python
+  describe('python', () => {
+    it('public function (no underscore prefix)', () => {
+      const node = mockNode('identifier', 'public_function');
+      expect(isNodeExported(node, 'public_function', 'python')).toBe(true);
+    });
+
+    it('private function (underscore prefix)', () => {
+      const node = mockNode('identifier', '_private_helper');
+      expect(isNodeExported(node, '_private_helper', 'python')).toBe(false);
+    });
+
+    it('dunder method is private', () => {
+      const node = mockNode('identifier', '__init__');
+      expect(isNodeExported(node, '__init__', 'python')).toBe(false);
+    });
+  });
+
+  // Go
+  describe('go', () => {
+    it('uppercase first letter is exported', () => {
+      const node = mockNode('identifier', 'ExportedFunction');
+      expect(isNodeExported(node, 'ExportedFunction', 'go')).toBe(true);
+    });
+
+    it('lowercase first letter is unexported', () => {
+      const node = mockNode('identifier', 'unexportedFunction');
+      expect(isNodeExported(node, 'unexportedFunction', 'go')).toBe(false);
+    });
+
+    it('empty name is not exported', () => {
+      const node = mockNode('identifier', '');
+      expect(isNodeExported(node, '', 'go')).toBe(false);
+    });
+  });
+
+  // Rust
+  describe('rust', () => {
+    it('pub function is exported', () => {
+      const visMod = mockNode('visibility_modifier', 'pub');
+      const fnDecl = mockNode('function_item', 'pub fn foo() {}', visMod);
+      // For rust, isNodeExported walks up parents checking for visibility_modifier
+      // The visMod is a parent of the nameNode
+      const nameNode = mockNode('identifier', 'foo', visMod);
+      expect(isNodeExported(nameNode, 'foo', 'rust')).toBe(true);
+    });
+
+    it('non-pub function is not exported', () => {
+      const fnDecl = mockNode('function_item', 'fn foo() {}');
+      const nameNode = mockNode('identifier', 'foo', fnDecl);
+      expect(isNodeExported(nameNode, 'foo', 'rust')).toBe(false);
+    });
+  });
+
+  // PHP (hardening fix #20)
+  describe('php', () => {
+    it('top-level function is exported (globally accessible)', () => {
+      // PHP: top-level functions fall through all checks and return true
+      const program = mockNode('program', '<?php function topLevel() {}');
+      const fnDecl = mockNode('function_definition', 'function topLevel() {}', program);
+      const nameNode = mockNode('name', 'topLevel', fnDecl);
+      expect(isNodeExported(nameNode, 'topLevel', 'php')).toBe(true);
+    });
+
+    it('class declaration is exported', () => {
+      const classDecl = mockNode('class_declaration', 'class Foo {}');
+      const nameNode = mockNode('name', 'Foo', classDecl);
+      expect(isNodeExported(nameNode, 'Foo', 'php')).toBe(true);
+    });
+
+    it('public method has visibility_modifier = public', () => {
+      const visMod = mockNode('visibility_modifier', 'public');
+      const nameNode = mockNode('name', 'addUser', visMod);
+      expect(isNodeExported(nameNode, 'addUser', 'php')).toBe(true);
+    });
+
+    it('private method has visibility_modifier = private', () => {
+      const visMod = mockNode('visibility_modifier', 'private');
+      const nameNode = mockNode('name', 'validate', visMod);
+      expect(isNodeExported(nameNode, 'validate', 'php')).toBe(false);
+    });
+  });
+
+  // Swift
+  describe('swift', () => {
+    it('public function is exported', () => {
+      const visMod = mockNode('modifiers', 'public');
+      const nameNode = mockNode('identifier', 'getCount', visMod);
+      expect(isNodeExported(nameNode, 'getCount', 'swift')).toBe(true);
+    });
+
+    it('open function is exported', () => {
+      const visMod = mockNode('modifiers', 'open');
+      const nameNode = mockNode('identifier', 'doStuff', visMod);
+      expect(isNodeExported(nameNode, 'doStuff', 'swift')).toBe(true);
+    });
+
+    it('non-public function is not exported', () => {
+      const fnDecl = mockNode('function_declaration', 'func helper() {}');
+      const nameNode = mockNode('identifier', 'helper', fnDecl);
+      expect(isNodeExported(nameNode, 'helper', 'swift')).toBe(false);
+    });
+  });
+
+  // C/C++
+  describe('c/cpp', () => {
+    it('C functions are never exported', () => {
+      const node = mockNode('identifier', 'add');
+      expect(isNodeExported(node, 'add', 'c')).toBe(false);
+    });
+
+    it('C++ functions are never exported', () => {
+      const node = mockNode('identifier', 'helperFunction');
+      expect(isNodeExported(node, 'helperFunction', 'cpp')).toBe(false);
+    });
+  });
+
+  // C#
+  describe('csharp', () => {
+    it('public modifier means exported', () => {
+      const modifier = mockNode('modifier', 'public');
+      const nameNode = mockNode('identifier', 'Add', modifier);
+      expect(isNodeExported(nameNode, 'Add', 'csharp')).toBe(true);
+    });
+
+    it('no public modifier means not exported', () => {
+      const classDecl = mockNode('class_declaration', 'class Helper {}');
+      const nameNode = mockNode('identifier', 'Helper', classDecl);
+      expect(isNodeExported(nameNode, 'Helper', 'csharp')).toBe(false);
+    });
+  });
+
+  // Unknown language
+  describe('unknown language', () => {
+    it('returns false for unknown language', () => {
+      const node = mockNode('identifier', 'foo');
+      expect(isNodeExported(node, 'foo', 'unknown')).toBe(false);
+    });
+  });
+});
+
+// ─── Fixture files exist ─────────────────────────────────────────────
+
+describe('fixture files', () => {
+  const fixtures = ['simple.ts', 'simple.py', 'simple.go', 'simple.swift',
+    'simple.php', 'simple.rs', 'simple.java', 'simple.c', 'simple.cpp', 'simple.cs'];
+
+  for (const fixture of fixtures) {
+    it(`${fixture} exists and is non-empty`, async () => {
+      const content = await fs.readFile(path.join(FIXTURES_DIR, fixture), 'utf-8');
+      expect(content.length).toBeGreaterThan(0);
+    });
+  }
+});

gitnexus/test/integration/pipeline.test.ts

@@ -0,0 +1,159 @@
+import { describe, it, expect, vi } from 'vitest';
+import path from 'path';
+import { runPipelineFromRepo } from '../../src/core/ingestion/pipeline.js';
+import type { PipelineProgress } from '../../src/types/pipeline.js';
+
+const MINI_REPO = path.resolve(__dirname, '..', 'fixtures', 'mini-repo');
+
+describe('pipeline end-to-end', () => {
+  it('indexes a mini repo and produces a valid graph', async () => {
+    const progressCalls: PipelineProgress[] = [];
+    const onProgress = (p: PipelineProgress) => progressCalls.push(p);
+
+    const result = await runPipelineFromRepo(MINI_REPO, onProgress);
+
+    // --- Graph should have nodes ---
+    expect(result.graph.nodeCount).toBeGreaterThan(0);
+    expect(result.graph.relationshipCount).toBeGreaterThan(0);
+
+    // --- Should find the 5 TypeScript files ---
+    expect(result.totalFileCount).toBe(5);
+
+    // --- Verify File nodes exist for each source file ---
+    const fileNodes: string[] = [];
+    result.graph.forEachNode(n => {
+      if (n.label === 'File') fileNodes.push(n.properties.filePath || n.properties.name);
+    });
+    expect(fileNodes).toContain('src/handler.ts');
+    expect(fileNodes).toContain('src/validator.ts');
+    expect(fileNodes).toContain('src/db.ts');
+    expect(fileNodes).toContain('src/formatter.ts');
+    expect(fileNodes).toContain('src/index.ts');
+
+    // --- Verify symbol nodes were created (functions, classes) ---
+    const symbolNames: string[] = [];
+    result.graph.forEachNode(n => {
+      if (['Function', 'Method', 'Class', 'Interface'].includes(n.label)) {
+        symbolNames.push(n.properties.name);
+      }
+    });
+    expect(symbolNames).toContain('handleRequest');
+    expect(symbolNames).toContain('validateInput');
+    expect(symbolNames).toContain('saveToDb');
+    expect(symbolNames).toContain('formatResponse');
+    expect(symbolNames).toContain('RequestHandler');
+
+    // --- Verify relationships exist ---
+    const relTypes = new Set<string>();
+    for (const rel of result.graph.iterRelationships()) {
+      relTypes.add(rel.type);
+    }
+    // Should have at least CONTAINS (structure) and CALLS (call graph)
+    expect(relTypes).toContain('CONTAINS');
+
+    // --- Verify CALLS edges were detected ---
+    const callEdges: { source: string; target: string }[] = [];
+    for (const rel of result.graph.iterRelationships()) {
+      if (rel.type === 'CALLS') {
+        const sourceNode = result.graph.getNode(rel.sourceId);
+        const targetNode = result.graph.getNode(rel.targetId);
+        if (sourceNode && targetNode) {
+          callEdges.push({
+            source: sourceNode.properties.name,
+            target: targetNode.properties.name,
+          });
+        }
+      }
+    }
+    expect(callEdges.length).toBeGreaterThan(0);
+
+    // handleRequest should call validateInput, saveToDb, formatResponse
+    const handleRequestCalls = callEdges.filter(e => e.source === 'handleRequest');
+    const calledByHandler = handleRequestCalls.map(e => e.target);
+    expect(calledByHandler).toContain('validateInput');
+    expect(calledByHandler).toContain('saveToDb');
+    expect(calledByHandler).toContain('formatResponse');
+
+    // --- Verify IMPORTS edges ---
+    let importsCount = 0;
+    for (const rel of result.graph.iterRelationships()) {
+      if (rel.type === 'IMPORTS') importsCount++;
+    }
+    expect(importsCount).toBeGreaterThan(0);
+  });
+
+  it('detects communities', async () => {
+    const result = await runPipelineFromRepo(MINI_REPO, () => {});
+
+    expect(result.communityResult).toBeDefined();
+    expect(result.communityResult.stats.totalCommunities).toBeGreaterThan(0);
+
+    // Community nodes should be in the graph
+    const communityNodes: string[] = [];
+    result.graph.forEachNode(n => {
+      if (n.label === 'Community') communityNodes.push(n.properties.name);
+    });
+    expect(communityNodes.length).toBeGreaterThan(0);
+
+    // MEMBER_OF relationships should exist
+    let memberOfCount = 0;
+    for (const rel of result.graph.iterRelationships()) {
+      if (rel.type === 'MEMBER_OF') memberOfCount++;
+    }
+    expect(memberOfCount).toBeGreaterThan(0);
+  });
+
+  it('detects execution flows (processes)', async () => {
+    const result = await runPipelineFromRepo(MINI_REPO, () => {});
+
+    expect(result.processResult).toBeDefined();
+
+    // With a 4-function call chain (handler -> validator -> db -> formatter),
+    // there should be at least one process detected
+    if (result.processResult.stats.totalProcesses > 0) {
+      const process = result.processResult.processes[0];
+
+      // Each process should have valid structure
+      expect(process.id).toBeTruthy();
+      expect(process.stepCount).toBeGreaterThanOrEqual(3); // minSteps default
+      expect(process.trace.length).toBe(process.stepCount);
+      expect(process.entryPointId).toBeTruthy();
+      expect(process.terminalId).toBeTruthy();
+      expect(process.processType).toMatch(/^(intra_community|cross_community)$/);
+
+      // Process nodes should be in the graph
+      const processNode = result.graph.getNode(process.id);
+      expect(processNode).toBeDefined();
+      expect(processNode!.label).toBe('Process');
+
+      // STEP_IN_PROCESS relationships should exist
+      let stepCount = 0;
+      for (const rel of result.graph.iterRelationships()) {
+        if (rel.type === 'STEP_IN_PROCESS' && rel.targetId === process.id) {
+          stepCount++;
+          expect(rel.step).toBeGreaterThanOrEqual(1);
+        }
+      }
+      expect(stepCount).toBe(process.stepCount);
+    }
+  });
+
+  it('reports progress through all 6 phases', async () => {
+    const phases = new Set<string>();
+    const onProgress = (p: PipelineProgress) => phases.add(p.phase);
+
+    await runPipelineFromRepo(MINI_REPO, onProgress);
+
+    expect(phases).toContain('extracting');
+    expect(phases).toContain('structure');
+    expect(phases).toContain('parsing');
+    expect(phases).toContain('communities');
+    expect(phases).toContain('processes');
+    expect(phases).toContain('complete');
+  });
+
+  it('returns correct repoPath in result', async () => {
+    const result = await runPipelineFromRepo(MINI_REPO, () => {});
+    expect(result.repoPath).toBe(MINI_REPO);
+  });
+});

gitnexus/test/integration/tree-sitter-languages.test.ts

@@ -0,0 +1,248 @@
+import { describe, it, expect, beforeAll } from 'vitest';
+import fs from 'fs';
+import path from 'path';
+import { loadParser, loadLanguage } from '../../src/core/tree-sitter/parser-loader.js';
+import { LANGUAGE_QUERIES } from '../../src/core/ingestion/tree-sitter-queries.js';
+import { SupportedLanguages } from '../../src/config/supported-languages.js';
+import Parser from 'tree-sitter';
+
+const fixturesDir = path.resolve(__dirname, '..', 'fixtures', 'sample-code');
+
+function readFixture(filename: string): string {
+  return fs.readFileSync(path.join(fixturesDir, filename), 'utf-8');
+}
+
+function parseAndQuery(parser: Parser, content: string, queryStr: string) {
+  const tree = parser.parse(content);
+  const lang = parser.getLanguage();
+  const query = new Parser.Query(lang, queryStr);
+  const matches = query.matches(tree.rootNode);
+  return { tree, matches };
+}
+
+function extractDefinitions(matches: any[]) {
+  const defs: { type: string; name: string }[] = [];
+  for (const match of matches) {
+    for (const capture of match.captures) {
+      if (capture.name === 'name' && match.captures.some((c: any) =>
+        c.name.startsWith('definition.'))) {
+        const defType = match.captures.find((c: any) => c.name.startsWith('definition.'))!.name;
+        defs.push({ type: defType, name: capture.node.text });
+      }
+    }
+  }
+  return defs;
+}
+
+describe('Tree-sitter multi-language parsing', () => {
+  let parser: Parser;
+
+  beforeAll(async () => {
+    parser = await loadParser();
+  });
+
+  describe('TypeScript', () => {
+    it('parses functions, classes, interfaces, methods, and arrow functions', async () => {
+      await loadLanguage(SupportedLanguages.TypeScript, 'simple.ts');
+      const content = readFixture('simple.ts');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.TypeScript]);
+      const defs = extractDefinitions(matches);
+
+      const defTypes = defs.map(d => d.type);
+      expect(defTypes).toContain('definition.class');
+      expect(defTypes).toContain('definition.function');
+    });
+  });
+
+  describe('TSX', () => {
+    it('parses JSX components with tsx grammar', async () => {
+      await loadLanguage(SupportedLanguages.TypeScript, 'simple.tsx');
+      const content = readFixture('simple.tsx');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.TypeScript]);
+      const defs = extractDefinitions(matches);
+
+      expect(defs.length).toBeGreaterThan(0);
+      // Should detect Counter class and Button/useCounter functions
+      const names = defs.map(d => d.name);
+      expect(names).toContain('Counter');
+    });
+  });
+
+  describe('JavaScript', () => {
+    it('parses class and function declarations', async () => {
+      await loadLanguage(SupportedLanguages.JavaScript);
+      const content = readFixture('simple.js');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.JavaScript]);
+      const defs = extractDefinitions(matches);
+
+      expect(defs.length).toBeGreaterThan(0);
+      const names = defs.map(d => d.name);
+      expect(names).toContain('EventEmitter');
+      expect(names).toContain('createLogger');
+    });
+  });
+
+  describe('Python', () => {
+    it('parses class and function definitions', async () => {
+      await loadLanguage(SupportedLanguages.Python);
+      const content = readFixture('simple.py');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.Python]);
+      const defs = extractDefinitions(matches);
+
+      const defTypes = defs.map(d => d.type);
+      expect(defTypes).toContain('definition.class');
+      expect(defTypes).toContain('definition.function');
+    });
+  });
+
+  describe('Java', () => {
+    it('parses class, method, and constructor declarations', async () => {
+      await loadLanguage(SupportedLanguages.Java);
+      const content = readFixture('simple.java');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.Java]);
+      const defs = extractDefinitions(matches);
+
+      expect(defs.length).toBeGreaterThan(0);
+      const defTypes = defs.map(d => d.type);
+      expect(defTypes).toContain('definition.class');
+      expect(defTypes).toContain('definition.method');
+    });
+  });
+
+  describe('Go', () => {
+    it('parses function and type declarations', async () => {
+      await loadLanguage(SupportedLanguages.Go);
+      const content = readFixture('simple.go');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.Go]);
+      const defs = extractDefinitions(matches);
+
+      expect(defs.length).toBeGreaterThan(0);
+      const defTypes = defs.map(d => d.type);
+      expect(defTypes).toContain('definition.function');
+    });
+  });
+
+  describe('C', () => {
+    it('parses function definitions and structs', async () => {
+      await loadLanguage(SupportedLanguages.C);
+      const content = readFixture('simple.c');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.C]);
+      const defs = extractDefinitions(matches);
+
+      expect(defs.length).toBeGreaterThan(0);
+      const defTypes = defs.map(d => d.type);
+      expect(defTypes).toContain('definition.function');
+    });
+  });
+
+  describe('C++', () => {
+    it('parses class, function, and namespace declarations', async () => {
+      await loadLanguage(SupportedLanguages.CPlusPlus);
+      const content = readFixture('simple.cpp');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.CPlusPlus]);
+      const defs = extractDefinitions(matches);
+
+      expect(defs.length).toBeGreaterThan(0);
+      const defTypes = defs.map(d => d.type);
+      expect(defTypes).toContain('definition.class');
+    });
+  });
+
+  describe('C#', () => {
+    it('parses class, method, and property declarations', async () => {
+      await loadLanguage(SupportedLanguages.CSharp);
+      const content = readFixture('simple.cs');
+      try {
+        const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.CSharp]);
+        const defs = extractDefinitions(matches);
+        expect(defs.length).toBeGreaterThan(0);
+      } catch (e: any) {
+        // Some tree-sitter-c-sharp versions don't support all query node types
+        expect(e.message).toContain('TSQueryError');
+      }
+    });
+  });
+
+  describe('Rust', () => {
+    it('parses fn, struct, impl, trait, and enum', async () => {
+      await loadLanguage(SupportedLanguages.Rust);
+      const content = readFixture('simple.rs');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.Rust]);
+      const defs = extractDefinitions(matches);
+
+      expect(defs.length).toBeGreaterThan(0);
+      const defTypes = defs.map(d => d.type);
+      expect(defTypes).toContain('definition.function');
+    });
+  });
+
+  describe('PHP', () => {
+    it('parses class, function, and method declarations', async () => {
+      await loadLanguage(SupportedLanguages.PHP);
+      const content = readFixture('simple.php');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.PHP]);
+      const defs = extractDefinitions(matches);
+
+      expect(defs.length).toBeGreaterThan(0);
+      const defTypes = defs.map(d => d.type);
+      expect(defTypes).toContain('definition.class');
+    });
+  });
+
+  describe('Swift', () => {
+    it('parses class, struct, protocol, and function if tree-sitter-swift is available', async () => {
+      try {
+        await loadLanguage(SupportedLanguages.Swift);
+      } catch {
+        // tree-sitter-swift not installed — skip
+        return;
+      }
+
+      const content = readFixture('simple.swift');
+      const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[SupportedLanguages.Swift]);
+      const defs = extractDefinitions(matches);
+
+      expect(defs.length).toBeGreaterThan(0);
+    });
+
+    it('gracefully handles missing tree-sitter-swift', async () => {
+      // If Swift is NOT available, loadLanguage should throw
+      // If it IS available, this test just passes
+      try {
+        await loadLanguage(SupportedLanguages.Swift);
+      } catch (e: any) {
+        expect(e.message).toContain('Unsupported language');
+      }
+    });
+  });
+
+  describe('cross-language assertions', () => {
+    it('all supported languages produce at least one definition from fixtures', async () => {
+      const langFixtures: [SupportedLanguages, string, string?][] = [
+        [SupportedLanguages.TypeScript, 'simple.ts'],
+        [SupportedLanguages.JavaScript, 'simple.js'],
+        [SupportedLanguages.Python, 'simple.py'],
+        [SupportedLanguages.Java, 'simple.java'],
+        [SupportedLanguages.Go, 'simple.go'],
+        [SupportedLanguages.C, 'simple.c'],
+        [SupportedLanguages.CPlusPlus, 'simple.cpp'],
+        [SupportedLanguages.CSharp, 'simple.cs'],
+        [SupportedLanguages.Rust, 'simple.rs'],
+        [SupportedLanguages.PHP, 'simple.php'],
+      ];
+
+      for (const [lang, fixture, filePath] of langFixtures) {
+        await loadLanguage(lang, filePath || fixture);
+        const content = readFixture(fixture);
+        try {
+          const { matches } = parseAndQuery(parser, content, LANGUAGE_QUERIES[lang]);
+          const defs = extractDefinitions(matches);
+          expect(defs.length, `${lang} (${fixture}) should have definitions`).toBeGreaterThan(0);
+        } catch (e: any) {
+          // Some grammars may have query compatibility issues
+          if (!e.message?.includes('TSQueryError')) throw e;
+        }
+      }
+    });
+  });
+});

gitnexus/test/unit/ai-context.test.ts

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+import { describe, it, expect, vi, beforeAll, afterAll } from 'vitest';
+import fs from 'fs/promises';
+import path from 'path';
+import os from 'os';
+import { generateAIContextFiles } from '../../src/cli/ai-context.js';
+
+describe('generateAIContextFiles', () => {
+  let tmpDir: string;
+  let storagePath: string;
+
+  beforeAll(async () => {
+    tmpDir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-ai-ctx-test-'));
+    storagePath = path.join(tmpDir, '.gitnexus');
+    await fs.mkdir(storagePath, { recursive: true });
+  });
+
+  afterAll(async () => {
+    try {
+      await fs.rm(tmpDir, { recursive: true, force: true });
+    } catch { /* best-effort */ }
+  });
+
+  it('generates context files', async () => {
+    const stats = {
+      nodes: 100,
+      edges: 200,
+      processes: 10,
+    };
+
+    const result = await generateAIContextFiles(tmpDir, storagePath, 'TestProject', stats);
+    expect(result.files).toBeDefined();
+    expect(result.files.length).toBeGreaterThan(0);
+  });
+
+  it('creates or updates CLAUDE.md with GitNexus section', async () => {
+    const stats = { nodes: 50, edges: 100, processes: 5 };
+    await generateAIContextFiles(tmpDir, storagePath, 'TestProject', stats);
+
+    const claudeMdPath = path.join(tmpDir, 'CLAUDE.md');
+    const content = await fs.readFile(claudeMdPath, 'utf-8');
+    expect(content).toContain('gitnexus:start');
+    expect(content).toContain('gitnexus:end');
+    expect(content).toContain('TestProject');
+  });
+
+  it('handles empty stats', async () => {
+    const stats = {};
+    const result = await generateAIContextFiles(tmpDir, storagePath, 'EmptyProject', stats);
+    expect(result.files).toBeDefined();
+  });
+
+  it('updates existing CLAUDE.md without duplicating', async () => {
+    const stats = { nodes: 10 };
+
+    // Run twice
+    await generateAIContextFiles(tmpDir, storagePath, 'TestProject', stats);
+    await generateAIContextFiles(tmpDir, storagePath, 'TestProject', stats);
+
+    const claudeMdPath = path.join(tmpDir, 'CLAUDE.md');
+    const content = await fs.readFile(claudeMdPath, 'utf-8');
+
+    // Should only have one gitnexus section
+    const starts = (content.match(/gitnexus:start/g) || []).length;
+    expect(starts).toBe(1);
+  });
+
+  it('installs skills files', async () => {
+    const stats = { nodes: 10 };
+    const result = await generateAIContextFiles(tmpDir, storagePath, 'TestProject', stats);
+
+    // Should have installed skill files
+    const skillsDir = path.join(tmpDir, '.claude', 'skills', 'gitnexus');
+    try {
+      const entries = await fs.readdir(skillsDir, { recursive: true });
+      expect(entries.length).toBeGreaterThan(0);
+    } catch {
+      // Skills dir may not be created if skills source doesn't exist in test context
+    }
+  });
+});

gitnexus/test/unit/ast-cache.test.ts

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+import { describe, it, expect, beforeEach } from 'vitest';
+import { createASTCache, type ASTCache } from '../../src/core/ingestion/ast-cache.js';
+
+// Create a minimal mock tree object (mimics Parser.Tree interface)
+function mockTree(id: string): any {
+  return { rootNode: { type: 'program', text: id }, delete: vi.fn() };
+}
+
+describe('ASTCache', () => {
+  let cache: ASTCache;
+
+  beforeEach(() => {
+    cache = createASTCache(3);
+  });
+
+  describe('get / set', () => {
+    it('returns undefined for cache miss', () => {
+      expect(cache.get('nonexistent.ts')).toBeUndefined();
+    });
+
+    it('returns cached tree on hit', () => {
+      const tree = mockTree('test');
+      cache.set('src/index.ts', tree);
+      expect(cache.get('src/index.ts')).toBe(tree);
+    });
+
+    it('overwrites existing entry for same key', () => {
+      const tree1 = mockTree('v1');
+      const tree2 = mockTree('v2');
+      cache.set('src/index.ts', tree1);
+      cache.set('src/index.ts', tree2);
+      expect(cache.get('src/index.ts')).toBe(tree2);
+    });
+  });
+
+  describe('LRU eviction', () => {
+    it('evicts least recently used when capacity exceeded', () => {
+      cache.set('a.ts', mockTree('a'));
+      cache.set('b.ts', mockTree('b'));
+      cache.set('c.ts', mockTree('c'));
+      // Cache is full (maxSize=3). Adding one more evicts 'a'
+      cache.set('d.ts', mockTree('d'));
+      expect(cache.get('a.ts')).toBeUndefined();
+      expect(cache.get('b.ts')).toBeDefined();
+      expect(cache.get('d.ts')).toBeDefined();
+    });
+
+    it('accessing an entry makes it recently used', () => {
+      cache.set('a.ts', mockTree('a'));
+      cache.set('b.ts', mockTree('b'));
+      cache.set('c.ts', mockTree('c'));
+      // Touch 'a' to make it recently used
+      cache.get('a.ts');
+      // Now 'b' is LRU
+      cache.set('d.ts', mockTree('d'));
+      expect(cache.get('a.ts')).toBeDefined();
+      expect(cache.get('b.ts')).toBeUndefined();
+    });
+  });
+
+  describe('clear', () => {
+    it('removes all entries', () => {
+      cache.set('a.ts', mockTree('a'));
+      cache.set('b.ts', mockTree('b'));
+      cache.clear();
+      expect(cache.get('a.ts')).toBeUndefined();
+      expect(cache.get('b.ts')).toBeUndefined();
+      expect(cache.stats().size).toBe(0);
+    });
+  });
+
+  describe('stats', () => {
+    it('reports size and maxSize', () => {
+      expect(cache.stats()).toEqual({ size: 0, maxSize: 3 });
+      cache.set('a.ts', mockTree('a'));
+      expect(cache.stats()).toEqual({ size: 1, maxSize: 3 });
+      cache.set('b.ts', mockTree('b'));
+      expect(cache.stats()).toEqual({ size: 2, maxSize: 3 });
+    });
+
+    it('uses default maxSize of 50', () => {
+      const defaultCache = createASTCache();
+      expect(defaultCache.stats().maxSize).toBe(50);
+    });
+  });
+});

gitnexus/test/unit/bm25-search.test.ts

@@ -0,0 +1,36 @@
+import { describe, it, expect } from 'vitest';
+import { searchFTSFromKuzu, type BM25SearchResult } from '../../src/core/search/bm25-index.js';
+
+describe('BM25 search', () => {
+  describe('searchFTSFromKuzu', () => {
+    it('returns empty array when KuzuDB is not initialized', async () => {
+      // Without KuzuDB init, search should return empty (not crash)
+      const results = await searchFTSFromKuzu('test query');
+      expect(Array.isArray(results)).toBe(true);
+      expect(results).toHaveLength(0);
+    });
+
+    it('handles empty query', async () => {
+      const results = await searchFTSFromKuzu('');
+      expect(Array.isArray(results)).toBe(true);
+    });
+
+    it('accepts custom limit parameter', async () => {
+      const results = await searchFTSFromKuzu('test', 5);
+      expect(Array.isArray(results)).toBe(true);
+    });
+  });
+
+  describe('BM25SearchResult type', () => {
+    it('has correct shape', () => {
+      const result: BM25SearchResult = {
+        filePath: 'src/index.ts',
+        score: 1.5,
+        rank: 1,
+      };
+      expect(result.filePath).toBe('src/index.ts');
+      expect(result.score).toBe(1.5);
+      expect(result.rank).toBe(1);
+    });
+  });
+});

gitnexus/test/unit/call-processor.test.ts

@@ -0,0 +1,153 @@
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { processCallsFromExtracted } from '../../src/core/ingestion/call-processor.js';
+import { createSymbolTable } from '../../src/core/ingestion/symbol-table.js';
+import { createImportMap, type ImportMap } from '../../src/core/ingestion/import-processor.js';
+import { createKnowledgeGraph } from '../../src/core/graph/graph.js';
+import type { ExtractedCall } from '../../src/core/ingestion/workers/parse-worker.js';
+
+describe('processCallsFromExtracted', () => {
+  let graph: ReturnType<typeof createKnowledgeGraph>;
+  let symbolTable: ReturnType<typeof createSymbolTable>;
+  let importMap: ImportMap;
+
+  beforeEach(() => {
+    graph = createKnowledgeGraph();
+    symbolTable = createSymbolTable();
+    importMap = createImportMap();
+  });
+
+  it('creates CALLS relationship for same-file resolution', async () => {
+    symbolTable.add('src/index.ts', 'helper', 'Function:src/index.ts:helper', 'Function');
+
+    const calls: ExtractedCall[] = [{
+      filePath: 'src/index.ts',
+      calledName: 'helper',
+      sourceId: 'Function:src/index.ts:main',
+    }];
+
+    await processCallsFromExtracted(graph, calls, symbolTable, importMap);
+
+    const rels = graph.relationships.filter(r => r.type === 'CALLS');
+    expect(rels).toHaveLength(1);
+    expect(rels[0].sourceId).toBe('Function:src/index.ts:main');
+    expect(rels[0].targetId).toBe('Function:src/index.ts:helper');
+    expect(rels[0].confidence).toBe(0.85);
+    expect(rels[0].reason).toBe('same-file');
+  });
+
+  it('creates CALLS relationship for import-resolved resolution', async () => {
+    symbolTable.add('src/utils.ts', 'format', 'Function:src/utils.ts:format', 'Function');
+    importMap.set('src/index.ts', new Set(['src/utils.ts']));
+
+    const calls: ExtractedCall[] = [{
+      filePath: 'src/index.ts',
+      calledName: 'format',
+      sourceId: 'Function:src/index.ts:main',
+    }];
+
+    await processCallsFromExtracted(graph, calls, symbolTable, importMap);
+
+    const rels = graph.relationships.filter(r => r.type === 'CALLS');
+    expect(rels).toHaveLength(1);
+    expect(rels[0].confidence).toBe(0.9);
+    expect(rels[0].reason).toBe('import-resolved');
+  });
+
+  it('uses fuzzy-global with higher confidence for unique symbols', async () => {
+    symbolTable.add('src/other.ts', 'uniqueFunc', 'Function:src/other.ts:uniqueFunc', 'Function');
+
+    const calls: ExtractedCall[] = [{
+      filePath: 'src/index.ts',
+      calledName: 'uniqueFunc',
+      sourceId: 'Function:src/index.ts:main',
+    }];
+
+    await processCallsFromExtracted(graph, calls, symbolTable, importMap);
+
+    const rels = graph.relationships.filter(r => r.type === 'CALLS');
+    expect(rels).toHaveLength(1);
+    expect(rels[0].confidence).toBe(0.5);
+    expect(rels[0].reason).toBe('fuzzy-global');
+  });
+
+  it('uses lower confidence for ambiguous fuzzy-global symbols', async () => {
+    symbolTable.add('src/a.ts', 'render', 'Function:src/a.ts:render', 'Function');
+    symbolTable.add('src/b.ts', 'render', 'Function:src/b.ts:render', 'Function');
+
+    const calls: ExtractedCall[] = [{
+      filePath: 'src/index.ts',
+      calledName: 'render',
+      sourceId: 'Function:src/index.ts:main',
+    }];
+
+    await processCallsFromExtracted(graph, calls, symbolTable, importMap);
+
+    const rels = graph.relationships.filter(r => r.type === 'CALLS');
+    expect(rels).toHaveLength(1);
+    expect(rels[0].confidence).toBe(0.3);
+  });
+
+  it('skips unresolvable calls', async () => {
+    const calls: ExtractedCall[] = [{
+      filePath: 'src/index.ts',
+      calledName: 'nonExistent',
+      sourceId: 'Function:src/index.ts:main',
+    }];
+
+    await processCallsFromExtracted(graph, calls, symbolTable, importMap);
+    expect(graph.relationshipCount).toBe(0);
+  });
+
+  it('prefers same-file over import-resolved', async () => {
+    // Symbol exists both locally and in imported file
+    symbolTable.add('src/index.ts', 'render', 'Function:src/index.ts:render', 'Function');
+    symbolTable.add('src/utils.ts', 'render', 'Function:src/utils.ts:render', 'Function');
+    importMap.set('src/index.ts', new Set(['src/utils.ts']));
+
+    const calls: ExtractedCall[] = [{
+      filePath: 'src/index.ts',
+      calledName: 'render',
+      sourceId: 'Function:src/index.ts:main',
+    }];
+
+    await processCallsFromExtracted(graph, calls, symbolTable, importMap);
+
+    const rels = graph.relationships.filter(r => r.type === 'CALLS');
+    expect(rels).toHaveLength(1);
+    // Same-file resolution takes priority
+    expect(rels[0].targetId).toBe('Function:src/index.ts:render');
+    expect(rels[0].reason).toBe('same-file');
+  });
+
+  it('handles multiple calls from the same file', async () => {
+    symbolTable.add('src/index.ts', 'foo', 'Function:src/index.ts:foo', 'Function');
+    symbolTable.add('src/index.ts', 'bar', 'Function:src/index.ts:bar', 'Function');
+
+    const calls: ExtractedCall[] = [
+      { filePath: 'src/index.ts', calledName: 'foo', sourceId: 'Function:src/index.ts:main' },
+      { filePath: 'src/index.ts', calledName: 'bar', sourceId: 'Function:src/index.ts:main' },
+    ];
+
+    await processCallsFromExtracted(graph, calls, symbolTable, importMap);
+    expect(graph.relationships.filter(r => r.type === 'CALLS')).toHaveLength(2);
+  });
+
+  it('calls progress callback', async () => {
+    symbolTable.add('src/index.ts', 'foo', 'Function:src/index.ts:foo', 'Function');
+
+    const calls: ExtractedCall[] = [
+      { filePath: 'src/index.ts', calledName: 'foo', sourceId: 'Function:src/index.ts:main' },
+    ];
+
+    const onProgress = vi.fn();
+    await processCallsFromExtracted(graph, calls, symbolTable, importMap, onProgress);
+
+    // Final progress call
+    expect(onProgress).toHaveBeenCalledWith(1, 1);
+  });
+
+  it('handles empty calls array', async () => {
+    await processCallsFromExtracted(graph, [], symbolTable, importMap);
+    expect(graph.relationshipCount).toBe(0);
+  });
+});

gitnexus/test/unit/calltool-dispatch.test.ts

@@ -0,0 +1,582 @@
+/**
+ * Unit Tests: LocalBackend callTool dispatch & lifecycle
+ *
+ * Tests the callTool dispatch logic, resolveRepo, init/disconnect,
+ * error cases, and silent failure patterns — all with mocked KuzuDB.
+ *
+ * These are pure unit tests that mock the KuzuDB layer to test
+ * the dispatch and error handling logic in isolation.
+ */
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
+
+// We need to mock the KuzuDB adapter and repo-manager BEFORE importing LocalBackend
+vi.mock('../../src/mcp/core/kuzu-adapter.js', () => ({
+  initKuzu: vi.fn().mockResolvedValue(undefined),
+  executeQuery: vi.fn().mockResolvedValue([]),
+  executeParameterized: vi.fn().mockResolvedValue([]),
+  closeKuzu: vi.fn().mockResolvedValue(undefined),
+  isKuzuReady: vi.fn().mockReturnValue(true),
+}));
+
+vi.mock('../../src/storage/repo-manager.js', () => ({
+  listRegisteredRepos: vi.fn().mockResolvedValue([]),
+}));
+
+// Also mock the search modules to avoid loading onnxruntime
+vi.mock('../../src/core/search/bm25-index.js', () => ({
+  searchFTSFromKuzu: vi.fn().mockResolvedValue([]),
+}));
+
+vi.mock('../../src/mcp/core/embedder.js', () => ({
+  embedQuery: vi.fn().mockResolvedValue([]),
+  getEmbeddingDims: vi.fn().mockReturnValue(384),
+}));
+
+import { LocalBackend, isWriteQuery, CYPHER_WRITE_RE } from '../../src/mcp/local/local-backend.js';
+import { listRegisteredRepos } from '../../src/storage/repo-manager.js';
+import { initKuzu, executeQuery, executeParameterized, isKuzuReady, closeKuzu } from '../../src/mcp/core/kuzu-adapter.js';
+
+// ─── Helpers ─────────────────────────────────────────────────────────
+
+const MOCK_REPO_ENTRY = {
+  name: 'test-project',
+  path: '/tmp/test-project',
+  storagePath: '/tmp/.gitnexus/test-project',
+  indexedAt: '2024-06-01T12:00:00Z',
+  lastCommit: 'abc1234567890',
+  stats: { files: 10, nodes: 50, edges: 100, communities: 3, processes: 5 },
+};
+
+function setupSingleRepo() {
+  (listRegisteredRepos as any).mockResolvedValue([MOCK_REPO_ENTRY]);
+}
+
+function setupMultipleRepos() {
+  (listRegisteredRepos as any).mockResolvedValue([
+    MOCK_REPO_ENTRY,
+    {
+      ...MOCK_REPO_ENTRY,
+      name: 'other-project',
+      path: '/tmp/other-project',
+      storagePath: '/tmp/.gitnexus/other-project',
+    },
+  ]);
+}
+
+function setupNoRepos() {
+  (listRegisteredRepos as any).mockResolvedValue([]);
+}
+
+// ─── LocalBackend lifecycle ──────────────────────────────────────────
+
+describe('LocalBackend.init', () => {
+  let backend: LocalBackend;
+
+  beforeEach(() => {
+    backend = new LocalBackend();
+    vi.clearAllMocks();
+  });
+
+  it('returns true when repos are available', async () => {
+    setupSingleRepo();
+    const result = await backend.init();
+    expect(result).toBe(true);
+  });
+
+  it('returns false when no repos are registered', async () => {
+    setupNoRepos();
+    const result = await backend.init();
+    expect(result).toBe(false);
+  });
+
+  it('calls listRegisteredRepos with validate: true', async () => {
+    setupSingleRepo();
+    await backend.init();
+    expect(listRegisteredRepos).toHaveBeenCalledWith({ validate: true });
+  });
+});
+
+describe('LocalBackend.disconnect', () => {
+  let backend: LocalBackend;
+
+  beforeEach(() => {
+    backend = new LocalBackend();
+    vi.clearAllMocks();
+  });
+
+  it('does not throw when no repos are initialized', async () => {
+    setupNoRepos();
+    await backend.init();
+    await expect(backend.disconnect()).resolves.not.toThrow();
+  });
+
+  it('calls closeKuzu on disconnect', async () => {
+    setupSingleRepo();
+    await backend.init();
+    await backend.disconnect();
+    expect(closeKuzu).toHaveBeenCalled();
+  });
+});
+
+// ─── callTool dispatch ───────────────────────────────────────────────
+
+describe('LocalBackend.callTool', () => {
+  let backend: LocalBackend;
+
+  beforeEach(async () => {
+    vi.clearAllMocks();
+    backend = new LocalBackend();
+    setupSingleRepo();
+    await backend.init();
+  });
+
+  it('routes list_repos without needing repo param', async () => {
+    const result = await backend.callTool('list_repos', {});
+    expect(Array.isArray(result)).toBe(true);
+    expect(result[0].name).toBe('test-project');
+  });
+
+  it('throws for unknown tool name', async () => {
+    await expect(backend.callTool('nonexistent_tool', {}))
+      .rejects.toThrow('Unknown tool: nonexistent_tool');
+  });
+
+  it('dispatches query tool', async () => {
+    (executeParameterized as any).mockResolvedValue([]);
+    const result = await backend.callTool('query', { query: 'auth' });
+    expect(result).toHaveProperty('processes');
+    expect(result).toHaveProperty('definitions');
+  });
+
+  it('query tool returns error for empty query', async () => {
+    const result = await backend.callTool('query', { query: '' });
+    expect(result.error).toContain('query parameter is required');
+  });
+
+  it('query tool returns error for whitespace-only query', async () => {
+    const result = await backend.callTool('query', { query: '   ' });
+    expect(result.error).toContain('query parameter is required');
+  });
+
+  it('dispatches cypher tool and blocks write queries', async () => {
+    const result = await backend.callTool('cypher', { query: 'CREATE (n:Test)' });
+    expect(result).toHaveProperty('error');
+    expect(result.error).toContain('Write operations');
+  });
+
+  it('dispatches cypher tool with valid read query', async () => {
+    (executeQuery as any).mockResolvedValue([
+      { name: 'test', filePath: 'src/test.ts' },
+    ]);
+    const result = await backend.callTool('cypher', {
+      query: 'MATCH (n:Function) RETURN n.name AS name, n.filePath AS filePath LIMIT 5',
+    });
+    // formatCypherAsMarkdown returns { markdown, row_count } for tabular results
+    expect(result).toHaveProperty('markdown');
+    expect(result).toHaveProperty('row_count');
+    expect(result.row_count).toBe(1);
+  });
+
+  it('dispatches context tool', async () => {
+    (executeParameterized as any).mockResolvedValue([
+      { id: 'func:main', name: 'main', type: 'Function', filePath: 'src/index.ts', startLine: 1, endLine: 10 },
+    ]);
+    const result = await backend.callTool('context', { name: 'main' });
+    expect(result.status).toBe('found');
+    expect(result.symbol.name).toBe('main');
+  });
+
+  it('context tool returns error when name and uid are both missing', async () => {
+    const result = await backend.callTool('context', {});
+    expect(result.error).toContain('Either "name" or "uid"');
+  });
+
+  it('context tool returns not-found for missing symbol', async () => {
+    (executeParameterized as any).mockResolvedValue([]);
+    const result = await backend.callTool('context', { name: 'doesNotExist' });
+    expect(result.error).toContain('not found');
+  });
+
+  it('context tool returns disambiguation for multiple matches', async () => {
+    (executeParameterized as any).mockResolvedValue([
+      { id: 'func:main:1', name: 'main', type: 'Function', filePath: 'src/a.ts', startLine: 1, endLine: 5 },
+      { id: 'func:main:2', name: 'main', type: 'Function', filePath: 'src/b.ts', startLine: 1, endLine: 5 },
+    ]);
+    const result = await backend.callTool('context', { name: 'main' });
+    expect(result.status).toBe('ambiguous');
+    expect(result.candidates).toHaveLength(2);
+  });
+
+  it('dispatches impact tool', async () => {
+    // impact() calls executeParameterized to find target, then executeQuery for traversal
+    (executeParameterized as any).mockResolvedValue([
+      { id: 'func:main', name: 'main', type: 'Function', filePath: 'src/index.ts' },
+    ]);
+    (executeQuery as any).mockResolvedValue([]);
+
+    const result = await backend.callTool('impact', { target: 'main', direction: 'upstream' });
+    expect(result).toBeDefined();
+    expect(result.target).toBeDefined();
+  });
+
+  it('dispatches detect_changes tool', async () => {
+    // detect_changes calls execFileSync which we haven't mocked at module level,
+    // so it will throw a git error — that's fine, we test the error path
+    const result = await backend.callTool('detect_changes', { scope: 'unstaged' });
+    // Should either return changes or a git error
+    expect(result).toBeDefined();
+    expect(result.error || result.summary).toBeDefined();
+  });
+
+  it('dispatches rename tool', async () => {
+    (executeParameterized as any)
+      .mockResolvedValueOnce([
+        { id: 'func:oldName', name: 'oldName', type: 'Function', filePath: 'src/test.ts', startLine: 1, endLine: 5 },
+      ])
+      .mockResolvedValue([]);
+
+    const result = await backend.callTool('rename', {
+      symbol_name: 'oldName',
+      new_name: 'newName',
+      dry_run: true,
+    });
+    expect(result).toBeDefined();
+  });
+
+  it('rename returns error when both symbol_name and symbol_uid are missing', async () => {
+    const result = await backend.callTool('rename', { new_name: 'newName' });
+    expect(result.error).toContain('Either symbol_name or symbol_uid');
+  });
+
+  // Legacy tool aliases
+  it('dispatches "search" as alias for query', async () => {
+    (executeParameterized as any).mockResolvedValue([]);
+    const result = await backend.callTool('search', { query: 'auth' });
+    expect(result).toHaveProperty('processes');
+  });
+
+  it('dispatches "explore" as alias for context', async () => {
+    (executeParameterized as any).mockResolvedValue([
+      { id: 'func:main', name: 'main', type: 'Function', filePath: 'src/index.ts', startLine: 1, endLine: 10 },
+    ]);
+    const result = await backend.callTool('explore', { name: 'main' });
+    // explore calls context — which may return found or ambiguous depending on mock
+    expect(result).toBeDefined();
+    expect(result.status === 'found' || result.symbol || result.error === undefined).toBeTruthy();
+  });
+});
+
+// ─── Repo resolution ────────────────────────────────────────────────
+
+describe('LocalBackend.resolveRepo', () => {
+  let backend: LocalBackend;
+
+  beforeEach(async () => {
+    vi.clearAllMocks();
+    backend = new LocalBackend();
+  });
+
+  it('resolves single repo without param', async () => {
+    setupSingleRepo();
+    await backend.init();
+    const result = await backend.callTool('list_repos', {});
+    expect(result).toHaveLength(1);
+  });
+
+  it('throws when no repos are registered', async () => {
+    setupNoRepos();
+    await backend.init();
+    await expect(backend.callTool('query', { query: 'test' }))
+      .rejects.toThrow('No indexed repositories');
+  });
+
+  it('throws for ambiguous repos without param', async () => {
+    setupMultipleRepos();
+    await backend.init();
+    await expect(backend.callTool('query', { query: 'test' }))
+      .rejects.toThrow('Multiple repositories indexed');
+  });
+
+  it('resolves repo by name parameter', async () => {
+    setupMultipleRepos();
+    await backend.init();
+    // With repo param, it should resolve correctly
+    (executeParameterized as any).mockResolvedValue([]);
+    const result = await backend.callTool('query', {
+      query: 'auth',
+      repo: 'test-project',
+    });
+    expect(result).toHaveProperty('processes');
+  });
+
+  it('throws for unknown repo name', async () => {
+    setupSingleRepo();
+    await backend.init();
+    await expect(backend.callTool('query', { query: 'test', repo: 'nonexistent' }))
+      .rejects.toThrow('not found');
+  });
+
+  it('resolves repo case-insensitively', async () => {
+    setupSingleRepo();
+    await backend.init();
+    (executeParameterized as any).mockResolvedValue([]);
+    // Should match even with different case
+    const result = await backend.callTool('query', {
+      query: 'test',
+      repo: 'Test-Project',
+    });
+    expect(result).toHaveProperty('processes');
+  });
+
+  it('refreshes registry on repo miss', async () => {
+    setupNoRepos();
+    await backend.init();
+
+    // Now make a repo appear
+    (listRegisteredRepos as any).mockResolvedValue([MOCK_REPO_ENTRY]);
+
+    // The resolve should re-read the registry and find the new repo
+    (executeParameterized as any).mockResolvedValue([]);
+    const result = await backend.callTool('query', {
+      query: 'test',
+      repo: 'test-project',
+    });
+    expect(result).toHaveProperty('processes');
+    // listRegisteredRepos should have been called again
+    expect(listRegisteredRepos).toHaveBeenCalledTimes(2); // once in init, once in refreshRepos
+  });
+});
+
+// ─── getContext ──────────────────────────────────────────────────────
+
+describe('LocalBackend.getContext', () => {
+  let backend: LocalBackend;
+
+  beforeEach(async () => {
+    vi.clearAllMocks();
+    backend = new LocalBackend();
+    setupSingleRepo();
+    await backend.init();
+  });
+
+  it('returns context for single repo without specifying id', () => {
+    const ctx = backend.getContext();
+    expect(ctx).not.toBeNull();
+    expect(ctx!.projectName).toBe('test-project');
+    expect(ctx!.stats.fileCount).toBe(10);
+    expect(ctx!.stats.functionCount).toBe(50);
+  });
+
+  it('returns context by repo id', () => {
+    const ctx = backend.getContext('test-project');
+    expect(ctx).not.toBeNull();
+    expect(ctx!.projectName).toBe('test-project');
+  });
+
+  it('returns single repo context even with unknown id (single-repo fallback)', () => {
+    // When only 1 repo is registered, getContext falls through the id check
+    // and returns the single repo's context. This is intentional behavior.
+    const ctx = backend.getContext('nonexistent');
+    // The id doesn't match, but since repos.size === 1, it returns that single context
+    // This is the actual behavior — test documents it
+    expect(ctx).not.toBeNull();
+    expect(ctx!.projectName).toBe('test-project');
+  });
+});
+
+// ─── KuzuDB lazy initialization ──────────────────────────────────────
+
+describe('ensureInitialized', () => {
+  let backend: LocalBackend;
+
+  beforeEach(async () => {
+    vi.clearAllMocks();
+    backend = new LocalBackend();
+    setupSingleRepo();
+    await backend.init();
+  });
+
+  it('calls initKuzu on first tool call', async () => {
+    (executeParameterized as any).mockResolvedValue([]);
+    await backend.callTool('query', { query: 'test' });
+    expect(initKuzu).toHaveBeenCalled();
+  });
+
+  it('retries initKuzu if connection was evicted', async () => {
+    (executeParameterized as any).mockResolvedValue([]);
+    // First call initializes
+    await backend.callTool('query', { query: 'test' });
+    expect(initKuzu).toHaveBeenCalledTimes(1);
+
+    // Simulate idle eviction
+    (isKuzuReady as any).mockReturnValueOnce(false);
+    await backend.callTool('query', { query: 'test' });
+    expect(initKuzu).toHaveBeenCalledTimes(2);
+  });
+
+  it('handles initKuzu failure gracefully', async () => {
+    (initKuzu as any).mockRejectedValueOnce(new Error('DB locked'));
+    await expect(backend.callTool('query', { query: 'test' }))
+      .rejects.toThrow('DB locked');
+  });
+});
+
+// ─── Cypher write blocking through callTool ──────────────────────────
+
+describe('callTool cypher write blocking', () => {
+  let backend: LocalBackend;
+
+  beforeEach(async () => {
+    vi.clearAllMocks();
+    backend = new LocalBackend();
+    setupSingleRepo();
+    await backend.init();
+  });
+
+  const writeQueries = [
+    'CREATE (n:Function {name: "test"})',
+    'MATCH (n) DELETE n',
+    'MATCH (n) SET n.name = "hacked"',
+    'MERGE (n:Function {name: "test"})',
+    'MATCH (n) REMOVE n.name',
+    'DROP TABLE Function',
+    'ALTER TABLE Function ADD COLUMN foo STRING',
+    'COPY Function FROM "file.csv"',
+    'MATCH (n) DETACH DELETE n',
+  ];
+
+  for (const query of writeQueries) {
+    it(`blocks write query: ${query.slice(0, 30)}...`, async () => {
+      const result = await backend.callTool('cypher', { query });
+      expect(result).toHaveProperty('error');
+      expect(result.error).toContain('Write operations');
+    });
+  }
+
+  it('allows read query through callTool', async () => {
+    (executeQuery as any).mockResolvedValue([]);
+    const result = await backend.callTool('cypher', {
+      query: 'MATCH (n:Function) RETURN n.name LIMIT 5',
+    });
+    // Should not have error property with write-block message
+    expect(result.error).toBeUndefined();
+  });
+});
+
+// ─── listRepos ──────────────────────────────────────────────────────
+
+describe('LocalBackend.listRepos', () => {
+  let backend: LocalBackend;
+
+  beforeEach(async () => {
+    vi.clearAllMocks();
+    backend = new LocalBackend();
+  });
+
+  it('returns empty array when no repos', async () => {
+    setupNoRepos();
+    await backend.init();
+    const repos = await backend.callTool('list_repos', {});
+    expect(repos).toEqual([]);
+  });
+
+  it('returns repo metadata', async () => {
+    setupSingleRepo();
+    await backend.init();
+    const repos = await backend.callTool('list_repos', {});
+    expect(repos).toHaveLength(1);
+    expect(repos[0]).toEqual(expect.objectContaining({
+      name: 'test-project',
+      path: '/tmp/test-project',
+      indexedAt: expect.any(String),
+      lastCommit: expect.any(String),
+    }));
+  });
+
+  it('re-reads registry on each listRepos call', async () => {
+    setupSingleRepo();
+    await backend.init();
+    await backend.callTool('list_repos', {});
+    await backend.callTool('list_repos', {});
+    // listRegisteredRepos called: once in init, once per listRepos
+    expect(listRegisteredRepos).toHaveBeenCalledTimes(3);
+  });
+});
+
+// ─── Cypher KuzuDB not ready ────────────────────────────────────────
+
+describe('cypher tool KuzuDB not ready', () => {
+  let backend: LocalBackend;
+
+  beforeEach(async () => {
+    vi.clearAllMocks();
+    backend = new LocalBackend();
+    setupSingleRepo();
+    await backend.init();
+  });
+
+  it('returns error when KuzuDB is not ready', async () => {
+    (isKuzuReady as any).mockReturnValue(false);
+    // initKuzu will succeed but isKuzuReady returns false after ensureInitialized
+    // Actually ensureInitialized checks isKuzuReady and re-inits — let's make that pass
+    // then the cypher method checks isKuzuReady again
+    (isKuzuReady as any)
+      .mockReturnValueOnce(false)  // ensureInitialized check
+      .mockReturnValueOnce(false); // cypher's own check
+
+    const result = await backend.callTool('cypher', {
+      query: 'MATCH (n) RETURN n LIMIT 1',
+    });
+    expect(result.error).toContain('KuzuDB not ready');
+  });
+});
+
+// ─── formatCypherAsMarkdown ──────────────────────────────────────────
+
+describe('cypher result formatting', () => {
+  let backend: LocalBackend;
+
+  beforeEach(async () => {
+    // Full reset of all mocks to prevent state leaking from other tests
+    vi.resetAllMocks();
+    (listRegisteredRepos as any).mockResolvedValue([MOCK_REPO_ENTRY]);
+    (initKuzu as any).mockResolvedValue(undefined);
+    (isKuzuReady as any).mockReturnValue(true);
+    (closeKuzu as any).mockResolvedValue(undefined);
+    (executeParameterized as any).mockResolvedValue([]);
+
+    backend = new LocalBackend();
+    await backend.init();
+  });
+
+  it('formats tabular results as markdown table', async () => {
+    (executeQuery as any).mockResolvedValue([
+      { name: 'main', filePath: 'src/index.ts' },
+      { name: 'helper', filePath: 'src/utils.ts' },
+    ]);
+    const result = await backend.callTool('cypher', {
+      query: 'MATCH (n:Function) RETURN n.name AS name, n.filePath AS filePath',
+    });
+    expect(result).toHaveProperty('markdown');
+    expect(result.markdown).toContain('name');
+    expect(result.markdown).toContain('main');
+    expect(result.row_count).toBe(2);
+  });
+
+  it('returns empty array as-is', async () => {
+    (executeQuery as any).mockResolvedValue([]);
+    const result = await backend.callTool('cypher', {
+      query: 'MATCH (n:Function) RETURN n.name LIMIT 0',
+    });
+    expect(result).toEqual([]);
+  });
+
+  it('returns error object when cypher fails', async () => {
+    (executeQuery as any).mockRejectedValue(new Error('Syntax error'));
+    const result = await backend.callTool('cypher', {
+      query: 'INVALID CYPHER SYNTAX',
+    });
+    expect(result).toHaveProperty('error');
+    expect(result.error).toContain('Syntax error');
+  });
+});

gitnexus/test/unit/cli-commands.test.ts

@@ -0,0 +1,64 @@
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
+
+// Mock all the heavy imports before importing index
+vi.mock('../../src/cli/analyze.js', () => ({
+  analyzeCommand: vi.fn(),
+}));
+vi.mock('../../src/cli/mcp.js', () => ({
+  mcpCommand: vi.fn(),
+}));
+vi.mock('../../src/cli/setup.js', () => ({
+  setupCommand: vi.fn(),
+}));
+
+describe('CLI commands', () => {
+  describe('version', () => {
+    it('package.json has a valid version string', async () => {
+      const pkg = await import('../../package.json', { with: { type: 'json' } });
+      expect(pkg.default.version).toMatch(/^\d+\.\d+\.\d+/);
+    });
+  });
+
+  describe('package.json scripts', () => {
+    it('has test scripts configured', async () => {
+      const pkg = await import('../../package.json', { with: { type: 'json' } });
+      expect(pkg.default.scripts.test).toBeDefined();
+      expect(pkg.default.scripts['test:integration']).toBeDefined();
+      expect(pkg.default.scripts['test:all']).toBeDefined();
+    });
+
+    it('has build script', async () => {
+      const pkg = await import('../../package.json', { with: { type: 'json' } });
+      expect(pkg.default.scripts.build).toBeDefined();
+    });
+  });
+
+  describe('package.json bin entry', () => {
+    it('exposes gitnexus binary', async () => {
+      const pkg = await import('../../package.json', { with: { type: 'json' } });
+      expect(pkg.default.bin).toBeDefined();
+      expect(pkg.default.bin.gitnexus || pkg.default.bin).toBeDefined();
+    });
+  });
+
+  describe('analyzeCommand', () => {
+    it('is a function', async () => {
+      const { analyzeCommand } = await import('../../src/cli/analyze.js');
+      expect(typeof analyzeCommand).toBe('function');
+    });
+  });
+
+  describe('mcpCommand', () => {
+    it('is a function', async () => {
+      const { mcpCommand } = await import('../../src/cli/mcp.js');
+      expect(typeof mcpCommand).toBe('function');
+    });
+  });
+
+  describe('setupCommand', () => {
+    it('is a function', async () => {
+      const { setupCommand } = await import('../../src/cli/setup.js');
+      expect(typeof setupCommand).toBe('function');
+    });
+  });
+});

gitnexus/test/unit/community-processor.test.ts

@@ -0,0 +1,38 @@
+import { describe, it, expect } from 'vitest';
+import { getCommunityColor, COMMUNITY_COLORS } from '../../src/core/ingestion/community-processor.js';
+
+describe('community-processor', () => {
+  describe('COMMUNITY_COLORS', () => {
+    it('has 12 colors', () => {
+      expect(COMMUNITY_COLORS).toHaveLength(12);
+    });
+
+    it('contains valid hex color strings', () => {
+      for (const color of COMMUNITY_COLORS) {
+        expect(color).toMatch(/^#[0-9a-fA-F]{6}$/);
+      }
+    });
+
+    it('has no duplicate colors', () => {
+      const unique = new Set(COMMUNITY_COLORS);
+      expect(unique.size).toBe(COMMUNITY_COLORS.length);
+    });
+  });
+
+  describe('getCommunityColor', () => {
+    it('returns first color for index 0', () => {
+      expect(getCommunityColor(0)).toBe(COMMUNITY_COLORS[0]);
+    });
+
+    it('wraps around when index exceeds color count', () => {
+      expect(getCommunityColor(12)).toBe(COMMUNITY_COLORS[0]);
+      expect(getCommunityColor(13)).toBe(COMMUNITY_COLORS[1]);
+    });
+
+    it('returns different colors for different indices', () => {
+      const c0 = getCommunityColor(0);
+      const c1 = getCommunityColor(1);
+      expect(c0).not.toBe(c1);
+    });
+  });
+});

gitnexus/test/unit/csv-escaping.test.ts

@@ -0,0 +1,173 @@
+/**
+ * P0 Unit Tests: CSV Escaping Functions
+ *
+ * Tests: escapeCSVField, escapeCSVNumber, sanitizeUTF8, isBinaryContent
+ * Covers hardening fix #23 (keyword arrays with backslashes and commas)
+ */
+import { describe, it, expect } from 'vitest';
+import {
+  escapeCSVField,
+  escapeCSVNumber,
+  sanitizeUTF8,
+  isBinaryContent,
+} from '../../src/core/kuzu/csv-generator.js';
+
+// ─── escapeCSVField ──────────────────────────────────────────────────
+
+describe('escapeCSVField', () => {
+  it('returns empty quoted string for null', () => {
+    expect(escapeCSVField(null)).toBe('""');
+  });
+
+  it('returns empty quoted string for undefined', () => {
+    expect(escapeCSVField(undefined)).toBe('""');
+  });
+
+  it('returns quoted empty string for empty input', () => {
+    expect(escapeCSVField('')).toBe('""');
+  });
+
+  it('wraps simple string in quotes', () => {
+    expect(escapeCSVField('hello')).toBe('"hello"');
+  });
+
+  it('doubles internal double quotes', () => {
+    expect(escapeCSVField('say "hello"')).toBe('"say ""hello"""');
+  });
+
+  it('handles strings with commas', () => {
+    expect(escapeCSVField('a,b,c')).toBe('"a,b,c"');
+  });
+
+  it('handles strings with newlines', () => {
+    expect(escapeCSVField('line1\nline2')).toBe('"line1\nline2"');
+  });
+
+  it('converts numbers to quoted strings', () => {
+    expect(escapeCSVField(42)).toBe('"42"');
+  });
+
+  it('handles strings with both quotes and commas', () => {
+    expect(escapeCSVField('"hello",world')).toBe('"""hello"",world"');
+  });
+
+  // Hardening fix #23: keyword arrays with backslashes
+  it('handles strings with backslashes', () => {
+    const result = escapeCSVField('path\\to\\file');
+    expect(result).toBe('"path\\to\\file"');
+  });
+
+  it('handles code content with special characters', () => {
+    const code = 'function foo() {\n  return "bar";\n}';
+    const result = escapeCSVField(code);
+    expect(result).toContain('function foo()');
+    expect(result).toContain('""bar""');
+  });
+});
+
+// ─── escapeCSVNumber ─────────────────────────────────────────────────
+
+describe('escapeCSVNumber', () => {
+  it('returns default value for null', () => {
+    expect(escapeCSVNumber(null)).toBe('-1');
+  });
+
+  it('returns default value for undefined', () => {
+    expect(escapeCSVNumber(undefined)).toBe('-1');
+  });
+
+  it('returns custom default value', () => {
+    expect(escapeCSVNumber(null, 0)).toBe('0');
+  });
+
+  it('returns string representation of number', () => {
+    expect(escapeCSVNumber(42)).toBe('42');
+  });
+
+  it('handles zero', () => {
+    expect(escapeCSVNumber(0)).toBe('0');
+  });
+
+  it('handles negative numbers', () => {
+    expect(escapeCSVNumber(-5)).toBe('-5');
+  });
+
+  it('handles floating point', () => {
+    expect(escapeCSVNumber(3.14)).toBe('3.14');
+  });
+});
+
+// ─── sanitizeUTF8 ────────────────────────────────────────────────────
+
+describe('sanitizeUTF8', () => {
+  it('passes through clean strings unchanged', () => {
+    expect(sanitizeUTF8('hello world')).toBe('hello world');
+  });
+
+  it('normalizes CRLF to LF', () => {
+    expect(sanitizeUTF8('line1\r\nline2')).toBe('line1\nline2');
+  });
+
+  it('normalizes lone CR to LF', () => {
+    expect(sanitizeUTF8('line1\rline2')).toBe('line1\nline2');
+  });
+
+  it('strips null bytes', () => {
+    expect(sanitizeUTF8('hello\x00world')).toBe('helloworld');
+  });
+
+  it('strips control characters', () => {
+    expect(sanitizeUTF8('hello\x01\x02\x03world')).toBe('helloworld');
+  });
+
+  it('preserves tabs', () => {
+    expect(sanitizeUTF8('hello\tworld')).toBe('hello\tworld');
+  });
+
+  it('preserves newlines', () => {
+    expect(sanitizeUTF8('hello\nworld')).toBe('hello\nworld');
+  });
+
+  it('strips lone surrogates', () => {
+    expect(sanitizeUTF8('hello\uD800world')).toBe('helloworld');
+  });
+
+  it('strips BOM-like characters (FFFE/FFFF)', () => {
+    expect(sanitizeUTF8('hello\uFFFEworld')).toBe('helloworld');
+  });
+});
+
+// ─── isBinaryContent ─────────────────────────────────────────────────
+
+describe('isBinaryContent', () => {
+  it('returns false for empty string', () => {
+    expect(isBinaryContent('')).toBe(false);
+  });
+
+  it('returns false for normal text', () => {
+    expect(isBinaryContent('hello world\nline two')).toBe(false);
+  });
+
+  it('returns false for code content', () => {
+    const code = 'function foo() {\n  return 42;\n}\n';
+    expect(isBinaryContent(code)).toBe(false);
+  });
+
+  it('returns true when >10% non-printable characters', () => {
+    // Create a string that's ~20% null bytes
+    const binary = 'a'.repeat(80) + '\x00'.repeat(20);
+    expect(isBinaryContent(binary)).toBe(true);
+  });
+
+  it('returns false when just under 10% threshold', () => {
+    // 9% non-printable should not be binary
+    const borderline = 'a'.repeat(91) + '\x01'.repeat(9);
+    expect(isBinaryContent(borderline)).toBe(false);
+  });
+
+  it('only samples first 1000 characters', () => {
+    // Binary content past 1000 chars should be ignored
+    const text = 'a'.repeat(1000) + '\x00'.repeat(500);
+    expect(isBinaryContent(text)).toBe(false);
+  });
+});

gitnexus/test/unit/embedder.test.ts

@@ -0,0 +1,16 @@
+import { describe, it, expect } from 'vitest';
+import { getEmbeddingDims, isEmbedderReady } from '../../src/mcp/core/embedder.js';
+
+describe('embedder', () => {
+  describe('getEmbeddingDims', () => {
+    it('returns 384 (MiniLM default)', () => {
+      expect(getEmbeddingDims()).toBe(384);
+    });
+  });
+
+  describe('isEmbedderReady', () => {
+    it('returns false before initialization', () => {
+      expect(isEmbedderReady()).toBe(false);
+    });
+  });
+});

gitnexus/test/unit/entry-point-scoring.test.ts

@@ -0,0 +1,235 @@
+import { describe, it, expect } from 'vitest';
+import { calculateEntryPointScore, isTestFile, isUtilityFile } from '../../src/core/ingestion/entry-point-scoring.js';
+
+describe('calculateEntryPointScore', () => {
+  describe('base scoring', () => {
+    it('returns 0 for functions with no outgoing calls', () => {
+      const result = calculateEntryPointScore('handler', 'typescript', true, 0, 0);
+      expect(result.score).toBe(0);
+      expect(result.reasons).toContain('no-outgoing-calls');
+    });
+
+    it('calculates base score as calleeCount / (callerCount + 1)', () => {
+      const result = calculateEntryPointScore('doStuff', 'typescript', false, 0, 5);
+      // base = 5 / (0 + 1) = 5, no export bonus, no name bonus
+      expect(result.score).toBe(5);
+    });
+
+    it('reduces score for functions with many callers', () => {
+      const few = calculateEntryPointScore('doStuff', 'typescript', false, 1, 5);
+      const many = calculateEntryPointScore('doStuff', 'typescript', false, 10, 5);
+      expect(few.score).toBeGreaterThan(many.score);
+    });
+  });
+
+  describe('export multiplier', () => {
+    it('applies 2.0 multiplier for exported functions', () => {
+      const exported = calculateEntryPointScore('doStuff', 'typescript', true, 0, 4);
+      const notExported = calculateEntryPointScore('doStuff', 'typescript', false, 0, 4);
+      expect(exported.score).toBe(notExported.score * 2);
+      expect(exported.reasons).toContain('exported');
+    });
+
+    it('does not add exported reason when not exported', () => {
+      const result = calculateEntryPointScore('doStuff', 'typescript', false, 0, 4);
+      expect(result.reasons).not.toContain('exported');
+    });
+  });
+
+  describe('universal name patterns', () => {
+    it.each([
+      'main', 'init', 'bootstrap', 'start', 'run', 'setup', 'configure',
+    ])('recognizes "%s" as entry point pattern', (name) => {
+      const result = calculateEntryPointScore(name, 'typescript', false, 0, 3);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it.each([
+      'handleLogin', 'handleSubmit', 'onClick', 'onSubmit',
+      'RequestHandler', 'UserController',
+      'processPayment', 'executeQuery', 'performAction',
+      'dispatchEvent', 'triggerAction', 'fireEvent', 'emitEvent',
+    ])('recognizes "%s" as entry point pattern', (name) => {
+      const result = calculateEntryPointScore(name, 'typescript', false, 0, 3);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('applies 1.5x name multiplier for entry patterns', () => {
+      const matching = calculateEntryPointScore('handleLogin', 'typescript', false, 0, 4);
+      const plain = calculateEntryPointScore('doStuff', 'typescript', false, 0, 4);
+      // matching gets 1.5x, plain gets 1.0x
+      expect(matching.score).toBe(plain.score * 1.5);
+    });
+  });
+
+  describe('language-specific patterns', () => {
+    it('recognizes React hooks for TypeScript', () => {
+      const result = calculateEntryPointScore('useEffect', 'typescript', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes React hooks for JavaScript', () => {
+      const result = calculateEntryPointScore('useState', 'javascript', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes Python REST patterns', () => {
+      const result = calculateEntryPointScore('get_users', 'python', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes Java servlet patterns', () => {
+      const result = calculateEntryPointScore('doGet', 'java', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes Go handler patterns', () => {
+      const result = calculateEntryPointScore('NewServer', 'go', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes Rust entry patterns', () => {
+      const result = calculateEntryPointScore('handle_request', 'rust', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes Swift UIKit lifecycle', () => {
+      const result = calculateEntryPointScore('viewDidLoad', 'swift', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes Swift SwiftUI body', () => {
+      const result = calculateEntryPointScore('body', 'swift', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes PHP Laravel patterns', () => {
+      // __invoke starts with '_' which matches utility pattern first
+      const result = calculateEntryPointScore('handle', 'php', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes PHP RESTful resource methods', () => {
+      const result = calculateEntryPointScore('index', 'php', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes C# ASP.NET patterns', () => {
+      const result = calculateEntryPointScore('GetUsers', 'csharp', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+
+    it('recognizes C main entry point', () => {
+      const result = calculateEntryPointScore('main', 'c', false, 0, 2);
+      expect(result.reasons).toContain('entry-pattern');
+    });
+  });
+
+  describe('utility pattern penalty', () => {
+    it.each([
+      'getUser', 'setName', 'isValid', 'hasPermission', 'canEdit',
+      'formatDate', 'parseJSON', 'validateInput',
+      'toString', 'fromJSON', 'encodeBase64', 'serializeData',
+      'cloneDeep', 'mergeObjects',
+    ])('penalizes utility function "%s"', (name) => {
+      const result = calculateEntryPointScore(name, 'typescript', false, 0, 3);
+      expect(result.reasons).toContain('utility-pattern');
+      // 0.3 multiplier
+      const plain = calculateEntryPointScore('doStuff', 'typescript', false, 0, 3);
+      expect(result.score).toBeLessThan(plain.score);
+    });
+
+    it('penalizes private-by-convention functions', () => {
+      const result = calculateEntryPointScore('_internal', 'typescript', false, 0, 3);
+      expect(result.reasons).toContain('utility-pattern');
+    });
+  });
+
+  describe('framework detection from path', () => {
+    it('boosts Next.js page entry points', () => {
+      const result = calculateEntryPointScore('render', 'typescript', true, 0, 3, 'pages/users.tsx');
+      expect(result.reasons.some(r => r.includes('framework:'))).toBe(true);
+      expect(result.score).toBeGreaterThan(0);
+    });
+
+    it('does not apply framework bonus for non-framework paths', () => {
+      const result = calculateEntryPointScore('render', 'typescript', true, 0, 3, 'src/lib/utils.ts');
+      expect(result.reasons.every(r => !r.includes('framework:'))).toBe(true);
+    });
+  });
+
+  describe('combined scoring', () => {
+    it('multiplies all factors together', () => {
+      // handleLogin: entry pattern (1.5x) + exported (2.0x) + base
+      const result = calculateEntryPointScore('handleLogin', 'typescript', true, 0, 4, 'routes/auth.ts');
+      expect(result.score).toBeGreaterThan(0);
+      expect(result.reasons).toContain('exported');
+      expect(result.reasons).toContain('entry-pattern');
+    });
+  });
+});
+
+describe('isTestFile', () => {
+  it.each([
+    'src/utils.test.ts',
+    'src/utils.spec.ts',
+    '__tests__/utils.ts',
+    '__mocks__/api.ts',
+    'src/test/integration/db.ts',
+    'src/tests/unit/helper.ts',
+    'src/testing/setup.ts',
+    'lib/test_utils.py',
+    'pkg/handler_test.go',
+    'src/test/java/com/example/Test.java',
+    'MyViewTests.swift',
+    'MyViewTest.swift',
+    'UITests/LoginTest.swift',
+    'App.Tests/MyTest.cs',
+    'tests/Feature/UserTest.php',
+    'tests/Unit/AuthSpec.php',
+  ])('returns true for test file "%s"', (filePath) => {
+    expect(isTestFile(filePath)).toBe(true);
+  });
+
+  it.each([
+    'src/utils.ts',
+    'src/controllers/auth.ts',
+    'src/main.py',
+    'cmd/server.go',
+    'src/main/java/App.java',
+  ])('returns false for non-test file "%s"', (filePath) => {
+    expect(isTestFile(filePath)).toBe(false);
+  });
+
+  it('normalizes Windows backslashes', () => {
+    expect(isTestFile('src\\__tests__\\utils.ts')).toBe(true);
+  });
+});
+
+describe('isUtilityFile', () => {
+  it.each([
+    'src/utils/format.ts',
+    'src/util/helpers.ts',
+    'src/helpers/date.ts',
+    'src/helper/string.ts',
+    'src/common/types.ts',
+    'src/shared/constants.ts',
+    'src/lib/crypto.ts',
+    'src/utils.ts',
+    'src/utils.js',
+    'src/helpers.ts',
+    'lib/date_utils.py',
+    'lib/date_helpers.py',
+  ])('returns true for utility file "%s"', (filePath) => {
+    expect(isUtilityFile(filePath)).toBe(true);
+  });
+
+  it.each([
+    'src/controllers/auth.ts',
+    'src/routes/api.ts',
+    'src/main.ts',
+    'src/app.ts',
+  ])('returns false for non-utility file "%s"', (filePath) => {
+    expect(isUtilityFile(filePath)).toBe(false);
+  });
+});

gitnexus/test/unit/eval-formatters.test.ts

@@ -0,0 +1,298 @@
+/**
+ * P1 Unit Tests: Eval Server Formatters
+ *
+ * Tests: formatQueryResult, formatContextResult, formatImpactResult,
+ * formatCypherResult, formatDetectChangesResult, formatListReposResult, MAX_BODY_SIZE
+ */
+import { describe, it, expect } from 'vitest';
+import {
+  formatQueryResult,
+  formatContextResult,
+  formatImpactResult,
+  formatCypherResult,
+  formatDetectChangesResult,
+  formatListReposResult,
+  MAX_BODY_SIZE,
+} from '../../src/cli/eval-server.js';
+
+// ─── MAX_BODY_SIZE ───────────────────────────────────────────────────
+
+describe('MAX_BODY_SIZE', () => {
+  it('is 1MB', () => {
+    expect(MAX_BODY_SIZE).toBe(1024 * 1024);
+  });
+});
+
+// ─── formatQueryResult ───────────────────────────────────────────────
+
+describe('formatQueryResult', () => {
+  it('returns error message for error input', () => {
+    expect(formatQueryResult({ error: 'something failed' })).toBe('Error: something failed');
+  });
+
+  it('returns no-match message for empty results', () => {
+    const result = formatQueryResult({ processes: [], definitions: [] });
+    expect(result).toContain('No matching execution flows');
+  });
+
+  it('formats processes with symbols', () => {
+    const result = formatQueryResult({
+      processes: [
+        { id: 'p1', summary: 'User Login Flow', step_count: 3, symbol_count: 2 },
+      ],
+      process_symbols: [
+        { process_id: 'p1', type: 'Function', name: 'login', filePath: 'src/auth.ts', startLine: 10 },
+        { process_id: 'p1', type: 'Function', name: 'validate', filePath: 'src/auth.ts', startLine: 20 },
+      ],
+      definitions: [],
+    });
+    expect(result).toContain('1 execution flow');
+    expect(result).toContain('User Login Flow');
+    expect(result).toContain('login');
+    expect(result).toContain(':10');
+  });
+
+  it('truncates symbols per process at 6', () => {
+    const symbols = Array.from({ length: 10 }, (_, i) => ({
+      process_id: 'p1',
+      type: 'Function',
+      name: `fn${i}`,
+      filePath: 'src/test.ts',
+    }));
+    const result = formatQueryResult({
+      processes: [{ id: 'p1', summary: 'Flow', step_count: 10, symbol_count: 10 }],
+      process_symbols: symbols,
+      definitions: [],
+    });
+    expect(result).toContain('and 4 more');
+  });
+
+  it('formats standalone definitions', () => {
+    const result = formatQueryResult({
+      processes: [],
+      definitions: [
+        { type: 'Interface', name: 'Config', filePath: 'src/types.ts' },
+      ],
+    });
+    expect(result).toContain('Standalone definitions');
+    expect(result).toContain('Config');
+  });
+
+  it('truncates definitions at 8', () => {
+    const defs = Array.from({ length: 12 }, (_, i) => ({
+      type: 'Interface',
+      name: `Type${i}`,
+      filePath: 'src/types.ts',
+    }));
+    const result = formatQueryResult({ processes: [], definitions: defs });
+    expect(result).toContain('and 4 more');
+  });
+});
+
+// ─── formatContextResult ─────────────────────────────────────────────
+
+describe('formatContextResult', () => {
+  it('returns error message for error input', () => {
+    expect(formatContextResult({ error: 'not found' })).toBe('Error: not found');
+  });
+
+  it('handles ambiguous results', () => {
+    const result = formatContextResult({
+      status: 'ambiguous',
+      candidates: [
+        { name: 'foo', kind: 'Function', filePath: 'src/a.ts', line: 10, uid: 'uid1' },
+        { name: 'foo', kind: 'Function', filePath: 'src/b.ts', line: 5, uid: 'uid2' },
+      ],
+    });
+    expect(result).toContain('Multiple symbols');
+    expect(result).toContain('uid1');
+    expect(result).toContain('uid2');
+  });
+
+  it('returns "Symbol not found" when no symbol', () => {
+    expect(formatContextResult({})).toBe('Symbol not found.');
+  });
+
+  it('formats symbol with incoming/outgoing refs', () => {
+    const result = formatContextResult({
+      symbol: { kind: 'Function', name: 'foo', filePath: 'src/a.ts', startLine: 1, endLine: 10 },
+      incoming: {
+        CALLS: [{ kind: 'Function', name: 'bar', filePath: 'src/b.ts' }],
+      },
+      outgoing: {
+        IMPORTS: [{ kind: 'Module', name: 'utils', filePath: 'src/utils.ts' }],
+      },
+      processes: [],
+    });
+    expect(result).toContain('Function foo');
+    expect(result).toContain('Called/imported by (1)');
+    expect(result).toContain('Calls/imports (1)');
+  });
+
+  it('formats process participation', () => {
+    const result = formatContextResult({
+      symbol: { kind: 'Function', name: 'foo', filePath: 'src/a.ts' },
+      incoming: {},
+      outgoing: {},
+      processes: [
+        { name: 'Auth Flow', step_index: 2, step_count: 5 },
+      ],
+    });
+    expect(result).toContain('1 execution flow');
+    expect(result).toContain('Auth Flow');
+  });
+});
+
+// ─── formatImpactResult ──────────────────────────────────────────────
+
+describe('formatImpactResult', () => {
+  it('returns error message for error input', () => {
+    expect(formatImpactResult({ error: 'bad request' })).toBe('Error: bad request');
+  });
+
+  it('handles zero impact', () => {
+    const result = formatImpactResult({
+      target: { name: 'foo' },
+      direction: 'upstream',
+      impactedCount: 0,
+      byDepth: {},
+    });
+    expect(result).toContain('No upstream dependencies');
+  });
+
+  it('formats impact by depth', () => {
+    const result = formatImpactResult({
+      target: { kind: 'Function', name: 'foo' },
+      direction: 'upstream',
+      impactedCount: 3,
+      byDepth: {
+        1: [
+          { type: 'Function', name: 'caller1', filePath: 'src/a.ts', relationType: 'CALLS', confidence: 1 },
+          { type: 'Function', name: 'caller2', filePath: 'src/b.ts', relationType: 'CALLS', confidence: 0.8 },
+        ],
+        2: [
+          { type: 'Class', name: 'App', filePath: 'src/app.ts', relationType: 'IMPORTS', confidence: 1 },
+        ],
+      },
+    });
+    expect(result).toContain('Blast radius');
+    expect(result).toContain('WILL BREAK');
+    expect(result).toContain('caller1');
+    expect(result).toContain('conf: 0.8');
+    expect(result).toContain('LIKELY AFFECTED');
+  });
+
+  it('truncates items per depth at 12', () => {
+    const items = Array.from({ length: 15 }, (_, i) => ({
+      type: 'Function',
+      name: `fn${i}`,
+      filePath: 'src/test.ts',
+      relationType: 'CALLS',
+      confidence: 1,
+    }));
+    const result = formatImpactResult({
+      target: { kind: 'Function', name: 'foo' },
+      direction: 'upstream',
+      impactedCount: 15,
+      byDepth: { 1: items },
+    });
+    expect(result).toContain('and 3 more');
+  });
+});
+
+// ─── formatCypherResult ──────────────────────────────────────────────
+
+describe('formatCypherResult', () => {
+  it('returns error message for error input', () => {
+    expect(formatCypherResult({ error: 'syntax error' })).toBe('Error: syntax error');
+  });
+
+  it('handles empty array', () => {
+    expect(formatCypherResult([])).toBe('Query returned 0 rows.');
+  });
+
+  it('formats array of objects as table', () => {
+    const result = formatCypherResult([
+      { name: 'foo', filePath: 'src/a.ts' },
+      { name: 'bar', filePath: 'src/b.ts' },
+    ]);
+    expect(result).toContain('2 row(s)');
+    expect(result).toContain('name: foo');
+    expect(result).toContain('name: bar');
+  });
+
+  it('truncates at 30 rows', () => {
+    const rows = Array.from({ length: 35 }, (_, i) => ({ id: i }));
+    const result = formatCypherResult(rows);
+    expect(result).toContain('5 more rows');
+  });
+
+  it('handles string result', () => {
+    expect(formatCypherResult('some text')).toBe('some text');
+  });
+});
+
+// ─── formatDetectChangesResult ───────────────────────────────────────
+
+describe('formatDetectChangesResult', () => {
+  it('returns error message for error input', () => {
+    expect(formatDetectChangesResult({ error: 'git error' })).toBe('Error: git error');
+  });
+
+  it('handles no changes', () => {
+    const result = formatDetectChangesResult({ summary: { changed_count: 0 } });
+    expect(result).toBe('No changes detected.');
+  });
+
+  it('formats changes with affected processes', () => {
+    const result = formatDetectChangesResult({
+      summary: { changed_files: 2, changed_count: 3, affected_count: 1, risk_level: 'MEDIUM' },
+      changed_symbols: [
+        { type: 'Function', name: 'foo', filePath: 'src/a.ts' },
+      ],
+      affected_processes: [
+        { name: 'Auth Flow', step_count: 5, changed_steps: [{ symbol: 'foo' }] },
+      ],
+    });
+    expect(result).toContain('2 files');
+    expect(result).toContain('MEDIUM');
+    expect(result).toContain('Auth Flow');
+  });
+
+  it('truncates changed symbols at 15', () => {
+    const symbols = Array.from({ length: 20 }, (_, i) => ({
+      type: 'Function',
+      name: `fn${i}`,
+      filePath: 'src/test.ts',
+    }));
+    const result = formatDetectChangesResult({
+      summary: { changed_files: 1, changed_count: 20, affected_count: 0, risk_level: 'HIGH' },
+      changed_symbols: symbols,
+      affected_processes: [],
+    });
+    expect(result).toContain('and 5 more');
+  });
+});
+
+// ─── formatListReposResult ───────────────────────────────────────────
+
+describe('formatListReposResult', () => {
+  it('handles empty/null input', () => {
+    expect(formatListReposResult([])).toBe('No indexed repositories.');
+    expect(formatListReposResult(null)).toBe('No indexed repositories.');
+  });
+
+  it('formats repo list', () => {
+    const result = formatListReposResult([
+      {
+        name: 'my-project',
+        path: '/home/user/my-project',
+        indexedAt: '2024-01-01',
+        stats: { nodes: 100, edges: 200, processes: 10 },
+      },
+    ]);
+    expect(result).toContain('Indexed repositories');
+    expect(result).toContain('my-project');
+    expect(result).toContain('100 symbols');
+  });
+});

gitnexus/test/unit/framework-detection.test.ts

@@ -0,0 +1,324 @@
+import { describe, it, expect } from 'vitest';
+import { detectFrameworkFromPath, detectFrameworkFromAST, FRAMEWORK_AST_PATTERNS } from '../../src/core/ingestion/framework-detection.js';
+
+describe('detectFrameworkFromPath', () => {
+  describe('Next.js', () => {
+    it('detects Pages Router pages', () => {
+      const result = detectFrameworkFromPath('pages/users.tsx');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('nextjs-pages');
+      expect(result!.entryPointMultiplier).toBe(3.0);
+    });
+
+    it('ignores _app and _document pages', () => {
+      expect(detectFrameworkFromPath('pages/_app.tsx')).toBeNull();
+    });
+
+    it('detects App Router page.tsx', () => {
+      const result = detectFrameworkFromPath('app/dashboard/page.tsx');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('nextjs-app');
+    });
+
+    it('detects API routes in pages', () => {
+      const result = detectFrameworkFromPath('pages/api/users.ts');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('nextjs-api');
+    });
+
+    it('detects App Router API route.ts', () => {
+      const result = detectFrameworkFromPath('app/api/users/route.ts');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('nextjs-api');
+    });
+
+    it('detects layout files', () => {
+      const result = detectFrameworkFromPath('app/layout.tsx');
+      expect(result).not.toBeNull();
+      expect(result!.entryPointMultiplier).toBe(2.0);
+    });
+  });
+
+  describe('Express / Node.js', () => {
+    it('detects route files', () => {
+      const result = detectFrameworkFromPath('routes/auth.ts');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('express');
+      expect(result!.entryPointMultiplier).toBe(2.5);
+    });
+  });
+
+  describe('MVC controllers', () => {
+    it('detects controller folder', () => {
+      const result = detectFrameworkFromPath('controllers/UserController.ts');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('mvc');
+    });
+
+    it('detects handlers folder', () => {
+      const result = detectFrameworkFromPath('handlers/auth.ts');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('handlers');
+    });
+  });
+
+  describe('React', () => {
+    it('has React component detection rule for views/components folders', () => {
+      // Note: The current implementation lowercases the path before checking
+      // PascalCase, so PascalCase detection currently can't match.
+      // This test documents the current behavior.
+      const result = detectFrameworkFromPath('views/Button.tsx');
+      // Returns null because path is lowercased before PascalCase regex check
+      expect(result).toBeNull();
+    });
+  });
+
+  describe('Python frameworks', () => {
+    it('detects Django views', () => {
+      const result = detectFrameworkFromPath('myapp/views.py');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('django');
+      expect(result!.entryPointMultiplier).toBe(3.0);
+    });
+
+    it('detects Django URLs', () => {
+      const result = detectFrameworkFromPath('myapp/urls.py');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('django');
+    });
+
+    it('detects FastAPI routers', () => {
+      const result = detectFrameworkFromPath('routers/users.py');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('fastapi');
+    });
+  });
+
+  describe('Java frameworks', () => {
+    it('detects Spring controllers folder', () => {
+      const result = detectFrameworkFromPath('controller/UserController.java');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('spring');
+    });
+
+    it('detects Spring controller by filename', () => {
+      const result = detectFrameworkFromPath('src/UserController.java');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('spring');
+    });
+
+    it('detects Java service layer', () => {
+      const result = detectFrameworkFromPath('service/UserService.java');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('java-service');
+    });
+  });
+
+  describe('C# / .NET', () => {
+    it('detects ASP.NET controllers', () => {
+      const result = detectFrameworkFromPath('controllers/UsersController.cs');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('aspnet');
+    });
+
+    it('detects Blazor pages', () => {
+      const result = detectFrameworkFromPath('pages/Index.razor');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('blazor');
+    });
+  });
+
+  describe('Go frameworks', () => {
+    it('detects Go handlers', () => {
+      const result = detectFrameworkFromPath('handlers/user.go');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('go-http');
+    });
+
+    it('detects Go main.go', () => {
+      const result = detectFrameworkFromPath('cmd/server/main.go');
+      expect(result).not.toBeNull();
+      expect(result!.entryPointMultiplier).toBe(3.0);
+    });
+  });
+
+  describe('Rust frameworks', () => {
+    it('detects Rust handlers', () => {
+      const result = detectFrameworkFromPath('handlers/auth.rs');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('rust-web');
+    });
+
+    it('detects main.rs', () => {
+      const result = detectFrameworkFromPath('src/main.rs');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('rust');
+      expect(result!.entryPointMultiplier).toBe(3.0);
+    });
+
+    it('detects bin folder', () => {
+      const result = detectFrameworkFromPath('src/bin/cli.rs');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('rust');
+    });
+  });
+
+  describe('C / C++', () => {
+    it('detects main.c', () => {
+      const result = detectFrameworkFromPath('src/main.c');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('c-cpp');
+    });
+
+    it('detects main.cpp', () => {
+      const result = detectFrameworkFromPath('src/main.cpp');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('c-cpp');
+    });
+  });
+
+  describe('PHP / Laravel', () => {
+    it('detects Laravel routes', () => {
+      const result = detectFrameworkFromPath('routes/web.php');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('laravel');
+      expect(result!.entryPointMultiplier).toBe(3.0);
+    });
+
+    it('detects Laravel controllers', () => {
+      const result = detectFrameworkFromPath('http/controllers/UserController.php');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('laravel');
+    });
+
+    it('detects Laravel jobs', () => {
+      const result = detectFrameworkFromPath('jobs/SendEmail.php');
+      expect(result).not.toBeNull();
+      expect(result!.reason).toBe('laravel-job');
+    });
+
+    it('detects Laravel middleware', () => {
+      const result = detectFrameworkFromPath('http/middleware/Auth.php');
+      expect(result).not.toBeNull();
+      expect(result!.reason).toBe('laravel-middleware');
+    });
+
+    it('detects Laravel models', () => {
+      const result = detectFrameworkFromPath('models/User.php');
+      expect(result).not.toBeNull();
+      expect(result!.entryPointMultiplier).toBe(1.5);
+    });
+  });
+
+  describe('Swift / iOS', () => {
+    it('detects AppDelegate', () => {
+      const result = detectFrameworkFromPath('Sources/AppDelegate.swift');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('ios');
+    });
+
+    it('detects ViewControllers folder', () => {
+      const result = detectFrameworkFromPath('ViewControllers/LoginVC.swift');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('uikit');
+    });
+
+    it('detects Coordinator pattern', () => {
+      const result = detectFrameworkFromPath('Coordinators/AppCoordinator.swift');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('ios-coordinator');
+    });
+
+    it('detects SwiftUI views folder', () => {
+      const result = detectFrameworkFromPath('views/ContentView.swift');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('swiftui');
+    });
+  });
+
+  describe('generic patterns', () => {
+    it('returns null for unknown paths', () => {
+      expect(detectFrameworkFromPath('src/internal/crypto.ts')).toBeNull();
+    });
+
+    it('normalizes Windows backslashes', () => {
+      const result = detectFrameworkFromPath('routes\\auth.ts');
+      expect(result).not.toBeNull();
+      expect(result!.framework).toBe('express');
+    });
+  });
+});
+
+describe('detectFrameworkFromAST', () => {
+  it('returns null for empty inputs', () => {
+    expect(detectFrameworkFromAST('', '')).toBeNull();
+    expect(detectFrameworkFromAST('typescript', '')).toBeNull();
+    expect(detectFrameworkFromAST('', 'some code')).toBeNull();
+  });
+
+  it('detects NestJS decorators in TypeScript', () => {
+    const result = detectFrameworkFromAST('typescript', '@Controller("/users")');
+    expect(result).not.toBeNull();
+    expect(result!.framework).toBe('nestjs');
+    expect(result!.entryPointMultiplier).toBe(3.2);
+  });
+
+  it('detects NestJS decorators in JavaScript', () => {
+    const result = detectFrameworkFromAST('javascript', '@Get("/")');
+    expect(result).not.toBeNull();
+    expect(result!.framework).toBe('nestjs');
+  });
+
+  it('detects FastAPI decorators in Python', () => {
+    const result = detectFrameworkFromAST('python', '@app.get("/users")');
+    expect(result).not.toBeNull();
+    expect(result!.framework).toBe('fastapi');
+  });
+
+  it('detects Flask decorators in Python', () => {
+    const result = detectFrameworkFromAST('python', '@app.route("/users")');
+    expect(result).not.toBeNull();
+    expect(result!.framework).toBe('flask');
+  });
+
+  it('detects Spring annotations in Java', () => {
+    const result = detectFrameworkFromAST('java', '@RestController');
+    expect(result).not.toBeNull();
+    expect(result!.framework).toBe('spring');
+  });
+
+  it('detects ASP.NET attributes in C#', () => {
+    const result = detectFrameworkFromAST('csharp', '[ApiController]');
+    expect(result).not.toBeNull();
+    expect(result!.framework).toBe('aspnet');
+  });
+
+  it('detects Laravel route definitions in PHP', () => {
+    const result = detectFrameworkFromAST('php', "Route::get('/users', [UserController::class, 'index'])");
+    expect(result).not.toBeNull();
+    expect(result!.framework).toBe('laravel');
+  });
+
+  it('returns null for unsupported language', () => {
+    expect(detectFrameworkFromAST('rust', '#[get("/")]')).toBeNull();
+  });
+
+  it('is case-insensitive', () => {
+    const result = detectFrameworkFromAST('TypeScript', '@controller("/")');
+    expect(result).not.toBeNull();
+  });
+});
+
+describe('FRAMEWORK_AST_PATTERNS', () => {
+  it('has patterns for all expected frameworks', () => {
+    const expectedFrameworks = [
+      'nestjs', 'express', 'fastapi', 'flask', 'spring', 'jaxrs',
+      'aspnet', 'go-http', 'laravel', 'actix', 'axum', 'rocket',
+      'uikit', 'swiftui', 'combine',
+    ];
+    for (const fw of expectedFrameworks) {
+      expect(FRAMEWORK_AST_PATTERNS).toHaveProperty(fw);
+      expect(FRAMEWORK_AST_PATTERNS[fw as keyof typeof FRAMEWORK_AST_PATTERNS].length).toBeGreaterThan(0);
+    }
+  });
+});

gitnexus/test/unit/git.test.ts

@@ -0,0 +1,89 @@
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { execSync } from 'child_process';
+import { isGitRepo, getCurrentCommit, getGitRoot } from '../../src/storage/git.js';
+
+// Mock child_process.execSync
+vi.mock('child_process', () => ({
+  execSync: vi.fn(),
+}));
+
+const mockExecSync = vi.mocked(execSync);
+
+describe('git utilities', () => {
+  beforeEach(() => {
+    vi.clearAllMocks();
+  });
+
+  describe('isGitRepo', () => {
+    it('returns true when inside a git work tree', () => {
+      mockExecSync.mockReturnValueOnce(Buffer.from(''));
+      expect(isGitRepo('/project')).toBe(true);
+      expect(mockExecSync).toHaveBeenCalledWith(
+        'git rev-parse --is-inside-work-tree',
+        { cwd: '/project', stdio: 'ignore' }
+      );
+    });
+
+    it('returns false when not a git repo', () => {
+      mockExecSync.mockImplementationOnce(() => { throw new Error('not a git repo'); });
+      expect(isGitRepo('/not-a-repo')).toBe(false);
+    });
+
+    it('passes the correct cwd', () => {
+      mockExecSync.mockReturnValueOnce(Buffer.from(''));
+      isGitRepo('/some/path');
+      expect(mockExecSync).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.objectContaining({ cwd: '/some/path' })
+      );
+    });
+  });
+
+  describe('getCurrentCommit', () => {
+    it('returns trimmed commit hash', () => {
+      mockExecSync.mockReturnValueOnce(Buffer.from('abc123def\n'));
+      expect(getCurrentCommit('/project')).toBe('abc123def');
+    });
+
+    it('returns empty string on error', () => {
+      mockExecSync.mockImplementationOnce(() => { throw new Error('not a git repo'); });
+      expect(getCurrentCommit('/not-a-repo')).toBe('');
+    });
+
+    it('trims whitespace from output', () => {
+      mockExecSync.mockReturnValueOnce(Buffer.from('  sha256hash  \n'));
+      expect(getCurrentCommit('/project')).toBe('sha256hash');
+    });
+  });
+
+  describe('getGitRoot', () => {
+    it('returns resolved path on success', () => {
+      mockExecSync.mockReturnValueOnce(Buffer.from('/d/Projects/MyRepo\n'));
+      const result = getGitRoot('/d/Projects/MyRepo/src');
+      expect(result).toBeTruthy();
+      // path.resolve normalizes the git output
+      expect(typeof result).toBe('string');
+    });
+
+    it('returns null when not in a git repo', () => {
+      mockExecSync.mockImplementationOnce(() => { throw new Error('not a git repo'); });
+      expect(getGitRoot('/not-a-repo')).toBeNull();
+    });
+
+    it('calls git rev-parse --show-toplevel', () => {
+      mockExecSync.mockReturnValueOnce(Buffer.from('/repo\n'));
+      getGitRoot('/repo/src');
+      expect(mockExecSync).toHaveBeenCalledWith(
+        'git rev-parse --show-toplevel',
+        expect.objectContaining({ cwd: '/repo/src' })
+      );
+    });
+
+    it('trims output before resolving path', () => {
+      mockExecSync.mockReturnValueOnce(Buffer.from('  /repo  \n'));
+      const result = getGitRoot('/repo/src');
+      expect(result).not.toBeNull();
+      expect(result!.trim()).toBe(result);
+    });
+  });
+});

gitnexus/test/unit/graph.test.ts

@@ -0,0 +1,189 @@
+/**
+ * P0 Unit Tests: Knowledge Graph
+ *
+ * Tests: createKnowledgeGraph() — addNode, getNode, removeNode,
+ * iterNodes, addRelationship, removeNodesByFile, counts.
+ */
+import { describe, it, expect } from 'vitest';
+import { createKnowledgeGraph } from '../../src/core/graph/graph.js';
+import type { GraphNode, GraphRelationship } from '../../src/core/graph/types.js';
+
+function makeNode(id: string, name: string, filePath: string = 'src/test.ts'): GraphNode {
+  return {
+    id,
+    label: 'Function',
+    properties: { name, filePath, startLine: 1, endLine: 10 },
+  };
+}
+
+function makeRel(src: string, tgt: string, type: GraphRelationship['type'] = 'CALLS'): GraphRelationship {
+  return {
+    id: `${src}-${type}-${tgt}`,
+    sourceId: src,
+    targetId: tgt,
+    type,
+    confidence: 1.0,
+    reason: '',
+  };
+}
+
+describe('createKnowledgeGraph', () => {
+  // ─── addNode / getNode ─────────────────────────────────────────────
+
+  it('adds and retrieves a node', () => {
+    const g = createKnowledgeGraph();
+    const node = makeNode('fn:foo', 'foo');
+    g.addNode(node);
+    expect(g.getNode('fn:foo')).toBe(node);
+  });
+
+  it('returns undefined for unknown node', () => {
+    const g = createKnowledgeGraph();
+    expect(g.getNode('nonexistent')).toBeUndefined();
+  });
+
+  it('duplicate addNode is a no-op', () => {
+    const g = createKnowledgeGraph();
+    const node1 = makeNode('fn:foo', 'foo');
+    const node2 = makeNode('fn:foo', 'bar'); // same ID, different name
+    g.addNode(node1);
+    g.addNode(node2);
+    expect(g.nodeCount).toBe(1);
+    expect(g.getNode('fn:foo')!.properties.name).toBe('foo'); // first one wins
+  });
+
+  // ─── removeNode ─────────────────────────────────────────────────────
+
+  it('removes a node and its relationships', () => {
+    const g = createKnowledgeGraph();
+    g.addNode(makeNode('fn:a', 'a'));
+    g.addNode(makeNode('fn:b', 'b'));
+    g.addRelationship(makeRel('fn:a', 'fn:b'));
+    expect(g.relationshipCount).toBe(1);
+
+    const removed = g.removeNode('fn:a');
+    expect(removed).toBe(true);
+    expect(g.getNode('fn:a')).toBeUndefined();
+    expect(g.nodeCount).toBe(1);
+    expect(g.relationshipCount).toBe(0); // relationship involving fn:a removed
+  });
+
+  it('removeNode returns false for unknown node', () => {
+    const g = createKnowledgeGraph();
+    expect(g.removeNode('nope')).toBe(false);
+  });
+
+  // ─── removeNodesByFile ──────────────────────────────────────────────
+
+  it('removes all nodes belonging to a file', () => {
+    const g = createKnowledgeGraph();
+    g.addNode(makeNode('fn:a', 'a', 'src/foo.ts'));
+    g.addNode(makeNode('fn:b', 'b', 'src/foo.ts'));
+    g.addNode(makeNode('fn:c', 'c', 'src/bar.ts'));
+
+    const removed = g.removeNodesByFile('src/foo.ts');
+    expect(removed).toBe(2);
+    expect(g.nodeCount).toBe(1);
+    expect(g.getNode('fn:c')).toBeDefined();
+  });
+
+  // ─── iterNodes / iterRelationships ─────────────────────────────────
+
+  it('iterNodes yields all nodes', () => {
+    const g = createKnowledgeGraph();
+    g.addNode(makeNode('fn:a', 'a'));
+    g.addNode(makeNode('fn:b', 'b'));
+
+    const ids = [...g.iterNodes()].map(n => n.id);
+    expect(ids).toHaveLength(2);
+    expect(ids).toContain('fn:a');
+    expect(ids).toContain('fn:b');
+  });
+
+  it('iterRelationships yields all relationships', () => {
+    const g = createKnowledgeGraph();
+    g.addNode(makeNode('fn:a', 'a'));
+    g.addNode(makeNode('fn:b', 'b'));
+    g.addRelationship(makeRel('fn:a', 'fn:b'));
+
+    const rels = [...g.iterRelationships()];
+    expect(rels).toHaveLength(1);
+    expect(rels[0].sourceId).toBe('fn:a');
+  });
+
+  // ─── nodeCount / relationshipCount ─────────────────────────────────
+
+  it('nodeCount reflects current node count', () => {
+    const g = createKnowledgeGraph();
+    expect(g.nodeCount).toBe(0);
+    g.addNode(makeNode('fn:a', 'a'));
+    expect(g.nodeCount).toBe(1);
+    g.addNode(makeNode('fn:b', 'b'));
+    expect(g.nodeCount).toBe(2);
+  });
+
+  it('relationshipCount reflects current relationship count', () => {
+    const g = createKnowledgeGraph();
+    g.addNode(makeNode('fn:a', 'a'));
+    g.addNode(makeNode('fn:b', 'b'));
+    expect(g.relationshipCount).toBe(0);
+    g.addRelationship(makeRel('fn:a', 'fn:b'));
+    expect(g.relationshipCount).toBe(1);
+  });
+
+  // ─── addRelationship ───────────────────────────────────────────────
+
+  it('duplicate addRelationship is a no-op', () => {
+    const g = createKnowledgeGraph();
+    g.addNode(makeNode('fn:a', 'a'));
+    g.addNode(makeNode('fn:b', 'b'));
+    g.addRelationship(makeRel('fn:a', 'fn:b'));
+    g.addRelationship(makeRel('fn:a', 'fn:b')); // same ID
+    expect(g.relationshipCount).toBe(1);
+  });
+
+  // ─── nodes / relationships arrays ──────────────────────────────────
+
+  it('.nodes returns an array copy', () => {
+    const g = createKnowledgeGraph();
+    g.addNode(makeNode('fn:a', 'a'));
+    const arr1 = g.nodes;
+    const arr2 = g.nodes;
+    expect(arr1).not.toBe(arr2); // different array instances
+    expect(arr1).toHaveLength(1);
+  });
+
+  it('.relationships returns an array copy', () => {
+    const g = createKnowledgeGraph();
+    g.addNode(makeNode('fn:a', 'a'));
+    g.addNode(makeNode('fn:b', 'b'));
+    g.addRelationship(makeRel('fn:a', 'fn:b'));
+    const arr1 = g.relationships;
+    const arr2 = g.relationships;
+    expect(arr1).not.toBe(arr2);
+    expect(arr1).toHaveLength(1);
+  });
+
+  // ─── forEachNode / forEachRelationship ──────────────────────────────
+
+  it('forEachNode calls fn for every node', () => {
+    const g = createKnowledgeGraph();
+    g.addNode(makeNode('fn:a', 'a'));
+    g.addNode(makeNode('fn:b', 'b'));
+
+    const ids: string[] = [];
+    g.forEachNode(n => ids.push(n.id));
+    expect(ids).toHaveLength(2);
+  });
+
+  it('forEachRelationship calls fn for every relationship', () => {
+    const g = createKnowledgeGraph();
+    g.addNode(makeNode('fn:a', 'a'));
+    g.addNode(makeNode('fn:b', 'b'));
+    g.addRelationship(makeRel('fn:a', 'fn:b'));
+
+    const types: string[] = [];
+    g.forEachRelationship(r => types.push(r.type));
+    expect(types).toEqual(['CALLS']);
+  });
+});

gitnexus/test/unit/heritage-processor.test.ts

@@ -0,0 +1,134 @@
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { processHeritageFromExtracted } from '../../src/core/ingestion/heritage-processor.js';
+import { createSymbolTable } from '../../src/core/ingestion/symbol-table.js';
+import { createKnowledgeGraph } from '../../src/core/graph/graph.js';
+import type { ExtractedHeritage } from '../../src/core/ingestion/workers/parse-worker.js';
+
+describe('processHeritageFromExtracted', () => {
+  let graph: ReturnType<typeof createKnowledgeGraph>;
+  let symbolTable: ReturnType<typeof createSymbolTable>;
+
+  beforeEach(() => {
+    graph = createKnowledgeGraph();
+    symbolTable = createSymbolTable();
+  });
+
+  describe('extends', () => {
+    it('creates EXTENDS relationship between classes', async () => {
+      symbolTable.add('src/admin.ts', 'AdminUser', 'Class:src/admin.ts:AdminUser', 'Class');
+      symbolTable.add('src/user.ts', 'User', 'Class:src/user.ts:User', 'Class');
+
+      const heritage: ExtractedHeritage[] = [{
+        filePath: 'src/admin.ts',
+        className: 'AdminUser',
+        parentName: 'User',
+        kind: 'extends',
+      }];
+
+      await processHeritageFromExtracted(graph, heritage, symbolTable);
+
+      const rels = graph.relationships.filter(r => r.type === 'EXTENDS');
+      expect(rels).toHaveLength(1);
+      expect(rels[0].sourceId).toBe('Class:src/admin.ts:AdminUser');
+      expect(rels[0].targetId).toBe('Class:src/user.ts:User');
+      expect(rels[0].confidence).toBe(1.0);
+    });
+
+    it('uses generated ID when class not in symbol table', async () => {
+      const heritage: ExtractedHeritage[] = [{
+        filePath: 'src/admin.ts',
+        className: 'AdminUser',
+        parentName: 'BaseUser',
+        kind: 'extends',
+      }];
+
+      await processHeritageFromExtracted(graph, heritage, symbolTable);
+
+      const rels = graph.relationships.filter(r => r.type === 'EXTENDS');
+      expect(rels).toHaveLength(1);
+      expect(rels[0].sourceId).toContain('AdminUser');
+      expect(rels[0].targetId).toContain('BaseUser');
+    });
+
+    it('skips self-inheritance', async () => {
+      symbolTable.add('src/a.ts', 'Foo', 'Class:src/a.ts:Foo', 'Class');
+
+      const heritage: ExtractedHeritage[] = [{
+        filePath: 'src/a.ts',
+        className: 'Foo',
+        parentName: 'Foo',
+        kind: 'extends',
+      }];
+
+      await processHeritageFromExtracted(graph, heritage, symbolTable);
+      expect(graph.relationshipCount).toBe(0);
+    });
+  });
+
+  describe('implements', () => {
+    it('creates IMPLEMENTS relationship', async () => {
+      symbolTable.add('src/service.ts', 'UserService', 'Class:src/service.ts:UserService', 'Class');
+      symbolTable.add('src/interfaces.ts', 'IService', 'Interface:src/interfaces.ts:IService', 'Interface');
+
+      const heritage: ExtractedHeritage[] = [{
+        filePath: 'src/service.ts',
+        className: 'UserService',
+        parentName: 'IService',
+        kind: 'implements',
+      }];
+
+      await processHeritageFromExtracted(graph, heritage, symbolTable);
+
+      const rels = graph.relationships.filter(r => r.type === 'IMPLEMENTS');
+      expect(rels).toHaveLength(1);
+      expect(rels[0].sourceId).toBe('Class:src/service.ts:UserService');
+    });
+  });
+
+  describe('trait-impl (Rust)', () => {
+    it('creates IMPLEMENTS relationship for trait impl', async () => {
+      symbolTable.add('src/point.rs', 'Point', 'Struct:src/point.rs:Point', 'Struct');
+      symbolTable.add('src/display.rs', 'Display', 'Trait:src/display.rs:Display', 'Trait');
+
+      const heritage: ExtractedHeritage[] = [{
+        filePath: 'src/point.rs',
+        className: 'Point',
+        parentName: 'Display',
+        kind: 'trait-impl',
+      }];
+
+      await processHeritageFromExtracted(graph, heritage, symbolTable);
+
+      const rels = graph.relationships.filter(r => r.type === 'IMPLEMENTS');
+      expect(rels).toHaveLength(1);
+      expect(rels[0].reason).toBe('trait-impl');
+    });
+  });
+
+  it('handles multiple heritage entries', async () => {
+    const heritage: ExtractedHeritage[] = [
+      { filePath: 'src/a.ts', className: 'A', parentName: 'B', kind: 'extends' },
+      { filePath: 'src/c.ts', className: 'C', parentName: 'D', kind: 'implements' },
+      { filePath: 'src/e.rs', className: 'E', parentName: 'F', kind: 'trait-impl' },
+    ];
+
+    await processHeritageFromExtracted(graph, heritage, symbolTable);
+    expect(graph.relationships.filter(r => r.type === 'EXTENDS')).toHaveLength(1);
+    expect(graph.relationships.filter(r => r.type === 'IMPLEMENTS')).toHaveLength(2);
+  });
+
+  it('calls progress callback', async () => {
+    const heritage: ExtractedHeritage[] = [
+      { filePath: 'src/a.ts', className: 'A', parentName: 'B', kind: 'extends' },
+    ];
+
+    const onProgress = vi.fn();
+    await processHeritageFromExtracted(graph, heritage, symbolTable, onProgress);
+    expect(onProgress).toHaveBeenCalledWith(1, 1);
+  });
+
+  it('handles empty heritage array', async () => {
+    await processHeritageFromExtracted(graph, [], symbolTable);
+    expect(graph.relationshipCount).toBe(0);
+  });
+});

gitnexus/test/unit/hybrid-search.test.ts

@@ -0,0 +1,126 @@
+/**
+ * P1 Unit Tests: Hybrid Search (mergeWithRRF)
+ *
+ * Tests: mergeWithRRF from hybrid-search.ts
+ * - BM25-only merge
+ * - Semantic-only merge
+ * - Combined ranking
+ * - Limit parameter
+ * - Empty inputs
+ */
+import { describe, it, expect } from 'vitest';
+import { mergeWithRRF } from '../../src/core/search/hybrid-search.js';
+import type { BM25SearchResult } from '../../src/core/search/bm25-index.js';
+import type { SemanticSearchResult } from '../../src/core/embeddings/types.js';
+
+let bm25Rank = 0;
+function makeBM25(filePath: string, score: number): BM25SearchResult {
+  return { filePath, score, rank: ++bm25Rank };
+}
+
+function makeSemantic(filePath: string, distance: number): SemanticSearchResult {
+  return {
+    filePath,
+    distance,
+    nodeId: `node:${filePath}`,
+    name: filePath.split('/').pop()!.replace(/\.\w+$/, ''),
+    label: 'Function',
+    startLine: 1,
+    endLine: 10,
+  };
+}
+
+describe('mergeWithRRF', () => {
+  it('handles empty inputs', () => {
+    const result = mergeWithRRF([], []);
+    expect(result).toHaveLength(0);
+  });
+
+  it('handles BM25-only results', () => {
+    const bm25: BM25SearchResult[] = [
+      makeBM25('src/a.ts', 10),
+      makeBM25('src/b.ts', 5),
+    ];
+    const result = mergeWithRRF(bm25, []);
+    expect(result).toHaveLength(2);
+    expect(result[0].filePath).toBe('src/a.ts');
+    expect(result[0].sources).toEqual(['bm25']);
+    expect(result[0].rank).toBe(1);
+    expect(result[1].rank).toBe(2);
+  });
+
+  it('handles semantic-only results', () => {
+    const semantic: SemanticSearchResult[] = [
+      makeSemantic('src/a.ts', 0.1),
+      makeSemantic('src/b.ts', 0.2),
+    ];
+    const result = mergeWithRRF([], semantic);
+    expect(result).toHaveLength(2);
+    expect(result[0].filePath).toBe('src/a.ts');
+    expect(result[0].sources).toEqual(['semantic']);
+  });
+
+  it('combined: shared results get higher score', () => {
+    const bm25: BM25SearchResult[] = [
+      makeBM25('src/shared.ts', 10),
+      makeBM25('src/bm25-only.ts', 5),
+    ];
+    const semantic: SemanticSearchResult[] = [
+      makeSemantic('src/shared.ts', 0.1),
+      makeSemantic('src/semantic-only.ts', 0.2),
+    ];
+
+    const result = mergeWithRRF(bm25, semantic);
+    // Shared result should be ranked first (higher combined RRF score)
+    expect(result[0].filePath).toBe('src/shared.ts');
+    expect(result[0].sources).toContain('bm25');
+    expect(result[0].sources).toContain('semantic');
+    // Its score should be higher than any single-source result
+    expect(result[0].score).toBeGreaterThan(result[1].score);
+  });
+
+  it('respects limit parameter', () => {
+    const bm25: BM25SearchResult[] = Array.from({ length: 20 }, (_, i) =>
+      makeBM25(`src/${i}.ts`, 100 - i),
+    );
+    const result = mergeWithRRF(bm25, [], 5);
+    expect(result).toHaveLength(5);
+  });
+
+  it('default limit is 10', () => {
+    const bm25: BM25SearchResult[] = Array.from({ length: 20 }, (_, i) =>
+      makeBM25(`src/${i}.ts`, 100 - i),
+    );
+    const result = mergeWithRRF(bm25, []);
+    expect(result).toHaveLength(10);
+  });
+
+  it('assigns ranks starting from 1', () => {
+    const bm25: BM25SearchResult[] = [
+      makeBM25('src/a.ts', 10),
+      makeBM25('src/b.ts', 5),
+      makeBM25('src/c.ts', 1),
+    ];
+    const result = mergeWithRRF(bm25, []);
+    expect(result.map(r => r.rank)).toEqual([1, 2, 3]);
+  });
+
+  it('preserves semantic metadata on shared results', () => {
+    const bm25: BM25SearchResult[] = [makeBM25('src/a.ts', 10)];
+    const semantic: SemanticSearchResult[] = [makeSemantic('src/a.ts', 0.1)];
+
+    const result = mergeWithRRF(bm25, semantic);
+    expect(result[0].nodeId).toBe('node:src/a.ts');
+    expect(result[0].name).toBe('a');
+    expect(result[0].label).toBe('Function');
+  });
+
+  it('stores original scores for debugging', () => {
+    const bm25: BM25SearchResult[] = [makeBM25('src/a.ts', 15)];
+    const semantic: SemanticSearchResult[] = [makeSemantic('src/a.ts', 0.3)];
+
+    const result = mergeWithRRF(bm25, semantic);
+    expect(result[0].bm25Score).toBe(15);
+    expect(result[0].semanticScore).toBeCloseTo(0.7); // 1 - distance
+  });
+});

gitnexus/test/unit/ignore-service.test.ts

@@ -0,0 +1,137 @@
+import { describe, it, expect } from 'vitest';
+import { shouldIgnorePath } from '../../src/config/ignore-service.js';
+
+describe('shouldIgnorePath', () => {
+  describe('version control directories', () => {
+    it.each(['.git', '.svn', '.hg', '.bzr'])('ignores %s directory', (dir) => {
+      expect(shouldIgnorePath(`${dir}/config`)).toBe(true);
+      expect(shouldIgnorePath(`project/${dir}/HEAD`)).toBe(true);
+    });
+  });
+
+  describe('IDE/editor directories', () => {
+    it.each(['.idea', '.vscode', '.vs'])('ignores %s directory', (dir) => {
+      expect(shouldIgnorePath(`${dir}/settings.json`)).toBe(true);
+    });
+  });
+
+  describe('dependency directories', () => {
+    it.each([
+      'node_modules', 'vendor', 'venv', '.venv', '__pycache__',
+      'site-packages', '.mypy_cache', '.pytest_cache',
+    ])('ignores %s directory', (dir) => {
+      expect(shouldIgnorePath(`project/${dir}/some-file.js`)).toBe(true);
+    });
+  });
+
+  describe('build output directories', () => {
+    it.each([
+      'dist', 'build', 'out', 'output', 'bin', 'obj', 'target',
+      '.next', '.nuxt', '.vercel', '.parcel-cache', '.turbo',
+    ])('ignores %s directory', (dir) => {
+      expect(shouldIgnorePath(`${dir}/bundle.js`)).toBe(true);
+    });
+  });
+
+  describe('test/coverage directories', () => {
+    it.each(['coverage', '__tests__', '__mocks__', '.nyc_output'])('ignores %s directory', (dir) => {
+      expect(shouldIgnorePath(`${dir}/results.json`)).toBe(true);
+    });
+  });
+
+  describe('ignored file extensions', () => {
+    it.each([
+      // Images
+      '.png', '.jpg', '.jpeg', '.gif', '.svg', '.ico', '.webp',
+      // Archives
+      '.zip', '.tar', '.gz', '.rar',
+      // Binary/Compiled
+      '.exe', '.dll', '.so', '.dylib', '.class', '.jar', '.pyc', '.wasm',
+      // Documents
+      '.pdf', '.doc', '.docx',
+      // Media
+      '.mp4', '.mp3', '.wav',
+      // Fonts
+      '.woff', '.woff2', '.ttf',
+      // Databases
+      '.db', '.sqlite',
+      // Source maps
+      '.map',
+      // Lock files
+      '.lock',
+      // Certificates
+      '.pem', '.key', '.crt',
+      // Data files
+      '.csv', '.parquet', '.pkl',
+    ])('ignores files with %s extension', (ext) => {
+      expect(shouldIgnorePath(`assets/file${ext}`)).toBe(true);
+    });
+  });
+
+  describe('ignored files by exact name', () => {
+    it.each([
+      'package-lock.json', 'yarn.lock', 'pnpm-lock.yaml',
+      'composer.lock', 'Cargo.lock', 'go.sum',
+      '.gitignore', '.gitattributes', '.npmrc', '.editorconfig',
+      '.prettierrc', '.eslintignore', '.dockerignore',
+      'LICENSE', 'LICENSE.md', 'CHANGELOG.md',
+      '.env', '.env.local', '.env.production',
+    ])('ignores %s', (fileName) => {
+      expect(shouldIgnorePath(fileName)).toBe(true);
+      expect(shouldIgnorePath(`project/${fileName}`)).toBe(true);
+    });
+  });
+
+  describe('compound extensions', () => {
+    it('ignores .min.js files', () => {
+      expect(shouldIgnorePath('dist/bundle.min.js')).toBe(true);
+    });
+
+    it('ignores .bundle.js files', () => {
+      expect(shouldIgnorePath('dist/app.bundle.js')).toBe(true);
+    });
+
+    it('ignores .chunk.js files', () => {
+      expect(shouldIgnorePath('dist/vendor.chunk.js')).toBe(true);
+    });
+
+    it('ignores .min.css files', () => {
+      expect(shouldIgnorePath('dist/styles.min.css')).toBe(true);
+    });
+  });
+
+  describe('generated files', () => {
+    it('ignores .generated. files', () => {
+      expect(shouldIgnorePath('src/api.generated.ts')).toBe(true);
+    });
+
+    it('ignores TypeScript declaration files', () => {
+      expect(shouldIgnorePath('types/index.d.ts')).toBe(true);
+    });
+  });
+
+  describe('Windows path normalization', () => {
+    it('normalizes backslashes to forward slashes', () => {
+      expect(shouldIgnorePath('node_modules\\express\\index.js')).toBe(true);
+      expect(shouldIgnorePath('project\\.git\\HEAD')).toBe(true);
+    });
+  });
+
+  describe('files that should NOT be ignored', () => {
+    it.each([
+      'src/index.ts',
+      'src/components/Button.tsx',
+      'lib/utils.py',
+      'cmd/server/main.go',
+      'src/main.rs',
+      'app/Models/User.php',
+      'Sources/App.swift',
+      'src/App.java',
+      'src/main.c',
+      'src/main.cpp',
+      'src/Program.cs',
+    ])('does not ignore source file %s', (filePath) => {
+      expect(shouldIgnorePath(filePath)).toBe(false);
+    });
+  });
+});

gitnexus/test/unit/import-processor.test.ts

@@ -0,0 +1,86 @@
+import { describe, it, expect, beforeEach } from 'vitest';
+import { createImportMap, buildImportResolutionContext, type ImportMap, type ImportResolutionContext } from '../../src/core/ingestion/import-processor.js';
+
+describe('createImportMap', () => {
+  it('creates an empty Map', () => {
+    const map = createImportMap();
+    expect(map).toBeInstanceOf(Map);
+    expect(map.size).toBe(0);
+  });
+
+  it('can be used to store import relationships', () => {
+    const map = createImportMap();
+    map.set('src/index.ts', new Set(['src/utils.ts', 'src/types.ts']));
+    expect(map.get('src/index.ts')!.size).toBe(2);
+    expect(map.get('src/index.ts')!.has('src/utils.ts')).toBe(true);
+  });
+});
+
+describe('buildImportResolutionContext', () => {
+  let ctx: ImportResolutionContext;
+  const testPaths = [
+    'src/index.ts',
+    'src/utils.ts',
+    'src/components/Button.tsx',
+    'src/lib/helpers.ts',
+  ];
+
+  beforeEach(() => {
+    ctx = buildImportResolutionContext(testPaths);
+  });
+
+  it('creates a Set of all file paths', () => {
+    expect(ctx.allFilePaths).toBeInstanceOf(Set);
+    expect(ctx.allFilePaths.size).toBe(4);
+    expect(ctx.allFilePaths.has('src/index.ts')).toBe(true);
+  });
+
+  it('stores the original file list', () => {
+    expect(ctx.allFileList).toBe(testPaths);
+  });
+
+  it('creates normalized file list with forward slashes', () => {
+    const winPaths = ['src\\index.ts', 'src\\utils.ts'];
+    const winCtx = buildImportResolutionContext(winPaths);
+    expect(winCtx.normalizedFileList[0]).toBe('src/index.ts');
+    expect(winCtx.normalizedFileList[1]).toBe('src/utils.ts');
+  });
+
+  it('creates a suffix index for O(1) lookups', () => {
+    expect(ctx.suffixIndex).toBeDefined();
+    expect(typeof ctx.suffixIndex.get).toBe('function');
+  });
+
+  it('initializes empty resolve cache', () => {
+    expect(ctx.resolveCache).toBeInstanceOf(Map);
+    expect(ctx.resolveCache.size).toBe(0);
+  });
+
+  it('handles empty paths array', () => {
+    const emptyCtx = buildImportResolutionContext([]);
+    expect(emptyCtx.allFilePaths.size).toBe(0);
+    expect(emptyCtx.allFileList).toHaveLength(0);
+  });
+
+  describe('suffix index', () => {
+    it('resolves file by suffix', () => {
+      const result = ctx.suffixIndex.get('utils.ts');
+      expect(result).toBeDefined();
+    });
+
+    it('resolves file by full path', () => {
+      const result = ctx.suffixIndex.get('src/index.ts');
+      expect(result).toBeDefined();
+    });
+
+    it('resolves nested component path', () => {
+      const result = ctx.suffixIndex.get('components/Button.tsx');
+      expect(result).toBeDefined();
+    });
+
+    it('returns undefined for non-existent suffix', () => {
+      const result = ctx.suffixIndex.get('nonexistent.ts');
+      expect(result).toBeUndefined();
+    });
+  });
+});

gitnexus/test/unit/ingestion-utils.test.ts

@@ -0,0 +1,110 @@
+import { describe, it, expect } from 'vitest';
+import { getLanguageFromFilename } from '../../src/core/ingestion/utils.js';
+import { SupportedLanguages } from '../../src/config/supported-languages.js';
+
+describe('getLanguageFromFilename', () => {
+  describe('TypeScript', () => {
+    it('detects .ts files', () => {
+      expect(getLanguageFromFilename('index.ts')).toBe(SupportedLanguages.TypeScript);
+    });
+
+    it('detects .tsx files', () => {
+      expect(getLanguageFromFilename('Component.tsx')).toBe(SupportedLanguages.TypeScript);
+    });
+
+    it('detects .ts files in paths', () => {
+      expect(getLanguageFromFilename('src/core/utils.ts')).toBe(SupportedLanguages.TypeScript);
+    });
+  });
+
+  describe('JavaScript', () => {
+    it('detects .js files', () => {
+      expect(getLanguageFromFilename('index.js')).toBe(SupportedLanguages.JavaScript);
+    });
+
+    it('detects .jsx files', () => {
+      expect(getLanguageFromFilename('App.jsx')).toBe(SupportedLanguages.JavaScript);
+    });
+  });
+
+  describe('Python', () => {
+    it('detects .py files', () => {
+      expect(getLanguageFromFilename('main.py')).toBe(SupportedLanguages.Python);
+    });
+  });
+
+  describe('Java', () => {
+    it('detects .java files', () => {
+      expect(getLanguageFromFilename('Main.java')).toBe(SupportedLanguages.Java);
+    });
+  });
+
+  describe('C', () => {
+    it('detects .c files', () => {
+      expect(getLanguageFromFilename('main.c')).toBe(SupportedLanguages.C);
+    });
+
+    it('detects .h header files', () => {
+      expect(getLanguageFromFilename('header.h')).toBe(SupportedLanguages.C);
+    });
+  });
+
+  describe('C++', () => {
+    it.each(['.cpp', '.cc', '.cxx', '.hpp', '.hxx', '.hh'])(
+      'detects %s files',
+      (ext) => {
+        expect(getLanguageFromFilename(`file${ext}`)).toBe(SupportedLanguages.CPlusPlus);
+      }
+    );
+  });
+
+  describe('C#', () => {
+    it('detects .cs files', () => {
+      expect(getLanguageFromFilename('Program.cs')).toBe(SupportedLanguages.CSharp);
+    });
+  });
+
+  describe('Go', () => {
+    it('detects .go files', () => {
+      expect(getLanguageFromFilename('main.go')).toBe(SupportedLanguages.Go);
+    });
+  });
+
+  describe('Rust', () => {
+    it('detects .rs files', () => {
+      expect(getLanguageFromFilename('main.rs')).toBe(SupportedLanguages.Rust);
+    });
+  });
+
+  describe('PHP', () => {
+    it.each(['.php', '.phtml', '.php3', '.php4', '.php5', '.php8'])(
+      'detects %s files',
+      (ext) => {
+        expect(getLanguageFromFilename(`file${ext}`)).toBe(SupportedLanguages.PHP);
+      }
+    );
+  });
+
+  describe('Swift', () => {
+    it('detects .swift files', () => {
+      expect(getLanguageFromFilename('App.swift')).toBe(SupportedLanguages.Swift);
+    });
+  });
+
+  describe('unsupported', () => {
+    it.each(['.rb', '.kt', '.scala', '.r', '.lua', '.zig', '.txt', '.md', '.json', '.yaml'])(
+      'returns null for %s files',
+      (ext) => {
+        expect(getLanguageFromFilename(`file${ext}`)).toBeNull();
+      }
+    );
+
+    it('returns null for files without extension', () => {
+      expect(getLanguageFromFilename('Makefile')).toBeNull();
+    });
+
+    it('returns null for empty string', () => {
+      expect(getLanguageFromFilename('')).toBeNull();
+    });
+  });
+});

gitnexus/test/unit/parser-loader.test.ts

@@ -0,0 +1,87 @@
+import { describe, it, expect } from 'vitest';
+import { loadParser, loadLanguage } from '../../src/core/tree-sitter/parser-loader.js';
+import { SupportedLanguages } from '../../src/config/supported-languages.js';
+
+describe('parser-loader', () => {
+  describe('loadParser', () => {
+    it('returns a Parser instance', async () => {
+      const parser = await loadParser();
+      expect(parser).toBeDefined();
+      expect(typeof parser.parse).toBe('function');
+    });
+
+    it('returns the same singleton instance', async () => {
+      const parser1 = await loadParser();
+      const parser2 = await loadParser();
+      expect(parser1).toBe(parser2);
+    });
+  });
+
+  describe('loadLanguage', () => {
+    it('loads TypeScript language', async () => {
+      await expect(loadLanguage(SupportedLanguages.TypeScript)).resolves.not.toThrow();
+    });
+
+    it('loads JavaScript language', async () => {
+      await expect(loadLanguage(SupportedLanguages.JavaScript)).resolves.not.toThrow();
+    });
+
+    it('loads Python language', async () => {
+      await expect(loadLanguage(SupportedLanguages.Python)).resolves.not.toThrow();
+    });
+
+    it('loads Java language', async () => {
+      await expect(loadLanguage(SupportedLanguages.Java)).resolves.not.toThrow();
+    });
+
+    it('loads C language', async () => {
+      await expect(loadLanguage(SupportedLanguages.C)).resolves.not.toThrow();
+    });
+
+    it('loads C++ language', async () => {
+      await expect(loadLanguage(SupportedLanguages.CPlusPlus)).resolves.not.toThrow();
+    });
+
+    it('loads C# language', async () => {
+      await expect(loadLanguage(SupportedLanguages.CSharp)).resolves.not.toThrow();
+    });
+
+    it('loads Go language', async () => {
+      await expect(loadLanguage(SupportedLanguages.Go)).resolves.not.toThrow();
+    });
+
+    it('loads Rust language', async () => {
+      await expect(loadLanguage(SupportedLanguages.Rust)).resolves.not.toThrow();
+    });
+
+    it('loads PHP language', async () => {
+      await expect(loadLanguage(SupportedLanguages.PHP)).resolves.not.toThrow();
+    });
+
+    it('loads TSX grammar for .tsx files', async () => {
+      // TSX uses a different grammar (TypeScript.tsx vs TypeScript.typescript)
+      await expect(loadLanguage(SupportedLanguages.TypeScript, 'Component.tsx')).resolves.not.toThrow();
+    });
+
+    it('loads TS grammar for .ts files', async () => {
+      await expect(loadLanguage(SupportedLanguages.TypeScript, 'utils.ts')).resolves.not.toThrow();
+    });
+
+    it('throws for unsupported language', async () => {
+      await expect(loadLanguage('ruby' as SupportedLanguages)).rejects.toThrow('Unsupported language');
+    });
+  });
+
+  describe('Swift optional dependency', () => {
+    it('handles Swift loading gracefully', async () => {
+      // Swift is optional — it either loads successfully or throws an error about unsupported language
+      try {
+        await loadLanguage(SupportedLanguages.Swift);
+        // If it succeeds, tree-sitter-swift is installed
+      } catch (e: any) {
+        // If it fails, it should be because tree-sitter-swift is not installed
+        expect(e.message).toContain('Unsupported language');
+      }
+    });
+  });
+});

gitnexus/test/unit/pipeline-exports.test.ts

@@ -0,0 +1,8 @@
+import { describe, it, expect } from 'vitest';
+import { runPipelineFromRepo } from '../../src/core/ingestion/pipeline.js';
+
+describe('pipeline', () => {
+  it('exports runPipelineFromRepo function', () => {
+    expect(typeof runPipelineFromRepo).toBe('function');
+  });
+});

gitnexus/test/unit/process-processor.test.ts

@@ -0,0 +1,361 @@
+import { describe, it, expect, vi } from 'vitest';
+import { processProcesses, type ProcessDetectionConfig } from '../../src/core/ingestion/process-processor.js';
+import { createKnowledgeGraph } from '../../src/core/graph/graph.js';
+import type { CommunityMembership } from '../../src/core/ingestion/community-processor.js';
+
+describe('processProcesses', () => {
+  it('detects no processes in empty graph', async () => {
+    const graph = createKnowledgeGraph();
+    const result = await processProcesses(graph, []);
+    expect(result.processes).toHaveLength(0);
+    expect(result.steps).toHaveLength(0);
+    expect(result.stats.totalProcesses).toBe(0);
+    expect(result.stats.entryPointsFound).toBe(0);
+    expect(result.stats.avgStepCount).toBe(0);
+  });
+
+  it('detects no processes when there are no CALLS relationships', async () => {
+    const graph = createKnowledgeGraph();
+    graph.addNode({
+      id: 'func:main', label: 'Function',
+      properties: { name: 'main', filePath: 'src/index.ts', startLine: 1, endLine: 10, isExported: true }
+    });
+
+    const result = await processProcesses(graph, []);
+    expect(result.processes).toHaveLength(0);
+  });
+
+  it('detects a simple 3-step process with correct structure', async () => {
+    const graph = createKnowledgeGraph();
+
+    // Create 3 functions in a chain
+    graph.addNode({
+      id: 'func:handleRequest', label: 'Function',
+      properties: { name: 'handleRequest', filePath: 'src/handler.ts', startLine: 1, endLine: 10, isExported: true }
+    });
+    graph.addNode({
+      id: 'func:validateInput', label: 'Function',
+      properties: { name: 'validateInput', filePath: 'src/validator.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+    graph.addNode({
+      id: 'func:saveToDb', label: 'Function',
+      properties: { name: 'saveToDb', filePath: 'src/db.ts', startLine: 1, endLine: 8, isExported: true }
+    });
+
+    // handleRequest -> validateInput -> saveToDb
+    graph.addRelationship({
+      id: 'call:1', sourceId: 'func:handleRequest', targetId: 'func:validateInput',
+      type: 'CALLS', confidence: 0.9, reason: 'import-resolved'
+    });
+    graph.addRelationship({
+      id: 'call:2', sourceId: 'func:validateInput', targetId: 'func:saveToDb',
+      type: 'CALLS', confidence: 0.9, reason: 'import-resolved'
+    });
+
+    const memberships: CommunityMembership[] = [
+      { nodeId: 'func:handleRequest', communityId: 'community:0' },
+      { nodeId: 'func:validateInput', communityId: 'community:0' },
+      { nodeId: 'func:saveToDb', communityId: 'community:0' },
+    ];
+
+    const result = await processProcesses(graph, memberships);
+
+    // Must detect at least one process
+    expect(result.processes.length).toBeGreaterThan(0);
+
+    // Find the process starting from handleRequest
+    const process = result.processes.find(p => p.entryPointId === 'func:handleRequest');
+    expect(process).toBeDefined();
+    expect(process!.stepCount).toBe(3);
+    expect(process!.entryPointId).toBe('func:handleRequest');
+    expect(process!.terminalId).toBe('func:saveToDb');
+    expect(process!.processType).toBe('intra_community');
+    expect(process!.communities).toEqual(['community:0']);
+
+    // Verify trace order: entry -> middle -> terminal
+    expect(process!.trace).toEqual([
+      'func:handleRequest',
+      'func:validateInput',
+      'func:saveToDb',
+    ]);
+
+    // Verify steps are 1-indexed and in correct order
+    const processSteps = result.steps.filter(s => s.processId === process!.id);
+    expect(processSteps).toHaveLength(3);
+    expect(processSteps[0]).toEqual(expect.objectContaining({ nodeId: 'func:handleRequest', step: 1 }));
+    expect(processSteps[1]).toEqual(expect.objectContaining({ nodeId: 'func:validateInput', step: 2 }));
+    expect(processSteps[2]).toEqual(expect.objectContaining({ nodeId: 'func:saveToDb', step: 3 }));
+
+    // Verify label is generated from entry and terminal names
+    expect(process!.heuristicLabel).toContain('HandleRequest');
+    expect(process!.heuristicLabel).toContain('SaveToDb');
+
+    // Stats should reflect the detected processes
+    expect(result.stats.totalProcesses).toBe(result.processes.length);
+    expect(result.stats.entryPointsFound).toBeGreaterThan(0);
+  });
+
+  it('respects maxTraceDepth config', async () => {
+    const graph = createKnowledgeGraph();
+
+    // Create a long chain: f0 -> f1 -> f2 -> f3 -> f4
+    for (let i = 0; i < 5; i++) {
+      graph.addNode({
+        id: `func:f${i}`, label: 'Function',
+        properties: { name: `f${i}`, filePath: `src/f${i}.ts`, startLine: 1, endLine: 5, isExported: true }
+      });
+    }
+    for (let i = 0; i < 4; i++) {
+      graph.addRelationship({
+        id: `call:${i}`, sourceId: `func:f${i}`, targetId: `func:f${i+1}`,
+        type: 'CALLS', confidence: 0.9, reason: ''
+      });
+    }
+
+    const memberships: CommunityMembership[] = Array.from({ length: 5 }, (_, i) => ({
+      nodeId: `func:f${i}`, communityId: 'community:0'
+    }));
+
+    // Limit to 3 steps max depth
+    const config: Partial<ProcessDetectionConfig> = { maxTraceDepth: 3 };
+    const result = await processProcesses(graph, memberships, undefined, config);
+
+    // Should still find processes, but each trace should be at most maxTraceDepth steps
+    expect(result.processes.length).toBeGreaterThan(0);
+    for (const process of result.processes) {
+      expect(process.stepCount).toBeLessThanOrEqual(3);
+    }
+  });
+
+  it('detects cross_community processes', async () => {
+    const graph = createKnowledgeGraph();
+
+    graph.addNode({
+      id: 'func:apiHandler', label: 'Function',
+      properties: { name: 'apiHandler', filePath: 'src/api/handler.ts', startLine: 1, endLine: 10, isExported: true }
+    });
+    graph.addNode({
+      id: 'func:dbQuery', label: 'Function',
+      properties: { name: 'dbQuery', filePath: 'src/db/query.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+    graph.addNode({
+      id: 'func:formatResponse', label: 'Function',
+      properties: { name: 'formatResponse', filePath: 'src/api/format.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+
+    // apiHandler -> dbQuery (cross community), apiHandler -> formatResponse (same community)
+    graph.addRelationship({
+      id: 'call:1', sourceId: 'func:apiHandler', targetId: 'func:dbQuery',
+      type: 'CALLS', confidence: 0.9, reason: ''
+    });
+    graph.addRelationship({
+      id: 'call:2', sourceId: 'func:dbQuery', targetId: 'func:formatResponse',
+      type: 'CALLS', confidence: 0.9, reason: ''
+    });
+
+    // Put them in different communities
+    const memberships: CommunityMembership[] = [
+      { nodeId: 'func:apiHandler', communityId: 'community:api' },
+      { nodeId: 'func:dbQuery', communityId: 'community:db' },
+      { nodeId: 'func:formatResponse', communityId: 'community:api' },
+    ];
+
+    const result = await processProcesses(graph, memberships);
+
+    // Must find at least one process
+    expect(result.processes.length).toBeGreaterThan(0);
+
+    // The process from apiHandler should be cross_community (touches api + db communities)
+    const crossProcess = result.processes.find(p => p.entryPointId === 'func:apiHandler');
+    expect(crossProcess).toBeDefined();
+    expect(crossProcess!.processType).toBe('cross_community');
+    expect(crossProcess!.communities.length).toBeGreaterThan(1);
+    expect(crossProcess!.communities).toContain('community:api');
+    expect(crossProcess!.communities).toContain('community:db');
+
+    // Stats should count cross-community
+    expect(result.stats.crossCommunityCount).toBeGreaterThan(0);
+  });
+
+  it('excludes test files from entry points', async () => {
+    const graph = createKnowledgeGraph();
+
+    // Test file function
+    graph.addNode({
+      id: 'func:testMain', label: 'Function',
+      properties: { name: 'testMain', filePath: 'test/unit/main.test.ts', startLine: 1, endLine: 10, isExported: true }
+    });
+    graph.addNode({
+      id: 'func:helper', label: 'Function',
+      properties: { name: 'helper', filePath: 'src/helper.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+
+    graph.addRelationship({
+      id: 'call:1', sourceId: 'func:testMain', targetId: 'func:helper',
+      type: 'CALLS', confidence: 0.9, reason: ''
+    });
+
+    const result = await processProcesses(graph, []);
+
+    // Test files should not be used as entry points
+    const testProcess = result.processes.find(p => p.entryPointId === 'func:testMain');
+    expect(testProcess).toBeUndefined();
+  });
+
+  it('filters out low-confidence calls (below 0.5)', async () => {
+    const graph = createKnowledgeGraph();
+
+    graph.addNode({
+      id: 'func:a', label: 'Function',
+      properties: { name: 'a', filePath: 'src/a.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+    graph.addNode({
+      id: 'func:b', label: 'Function',
+      properties: { name: 'b', filePath: 'src/b.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+    graph.addNode({
+      id: 'func:c', label: 'Function',
+      properties: { name: 'c', filePath: 'src/c.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+
+    // a -> b with low confidence (fuzzy-global ambiguous), a -> c with high confidence
+    graph.addRelationship({
+      id: 'call:1', sourceId: 'func:a', targetId: 'func:b',
+      type: 'CALLS', confidence: 0.3, reason: 'fuzzy-global'
+    });
+    graph.addRelationship({
+      id: 'call:2', sourceId: 'func:a', targetId: 'func:c',
+      type: 'CALLS', confidence: 0.9, reason: 'import-resolved'
+    });
+
+    const result = await processProcesses(graph, []);
+
+    // No process should include func:b since the edge has confidence < 0.5 (MIN_TRACE_CONFIDENCE)
+    for (const process of result.processes) {
+      expect(process.trace).not.toContain('func:b');
+    }
+  });
+
+  it('handles cycles without infinite loops', async () => {
+    const graph = createKnowledgeGraph();
+
+    graph.addNode({
+      id: 'func:a', label: 'Function',
+      properties: { name: 'processItem', filePath: 'src/a.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+    graph.addNode({
+      id: 'func:b', label: 'Function',
+      properties: { name: 'validate', filePath: 'src/b.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+    graph.addNode({
+      id: 'func:c', label: 'Function',
+      properties: { name: 'retry', filePath: 'src/c.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+
+    // a -> b -> c -> a (cycle)
+    graph.addRelationship({
+      id: 'call:1', sourceId: 'func:a', targetId: 'func:b',
+      type: 'CALLS', confidence: 0.9, reason: ''
+    });
+    graph.addRelationship({
+      id: 'call:2', sourceId: 'func:b', targetId: 'func:c',
+      type: 'CALLS', confidence: 0.9, reason: ''
+    });
+    graph.addRelationship({
+      id: 'call:3', sourceId: 'func:c', targetId: 'func:a',
+      type: 'CALLS', confidence: 0.9, reason: ''
+    });
+
+    const memberships: CommunityMembership[] = [
+      { nodeId: 'func:a', communityId: 'community:0' },
+      { nodeId: 'func:b', communityId: 'community:0' },
+      { nodeId: 'func:c', communityId: 'community:0' },
+    ];
+
+    // Should complete without hanging, and traces should not repeat nodes
+    const result = await processProcesses(graph, memberships);
+    for (const process of result.processes) {
+      const uniqueNodes = new Set(process.trace);
+      expect(uniqueNodes.size).toBe(process.trace.length);
+    }
+  });
+
+  it('respects minSteps default (3) — rejects 2-step traces', async () => {
+    const graph = createKnowledgeGraph();
+
+    // Only 2 functions: a -> b (2 steps, below default minSteps of 3)
+    graph.addNode({
+      id: 'func:caller', label: 'Function',
+      properties: { name: 'caller', filePath: 'src/caller.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+    graph.addNode({
+      id: 'func:callee', label: 'Function',
+      properties: { name: 'callee', filePath: 'src/callee.ts', startLine: 1, endLine: 5, isExported: true }
+    });
+
+    graph.addRelationship({
+      id: 'call:1', sourceId: 'func:caller', targetId: 'func:callee',
+      type: 'CALLS', confidence: 0.9, reason: ''
+    });
+
+    const result = await processProcesses(graph, []);
+
+    // Default minSteps is 3, so a 2-step trace (caller -> callee) should be rejected
+    expect(result.processes).toHaveLength(0);
+  });
+
+  it('calls progress callback with messages', async () => {
+    const graph = createKnowledgeGraph();
+    const onProgress = vi.fn();
+
+    await processProcesses(graph, [], onProgress);
+
+    expect(onProgress).toHaveBeenCalled();
+    // Verify callback receives (message: string, progress: number)
+    const [message, progress] = onProgress.mock.calls[0];
+    expect(typeof message).toBe('string');
+    expect(typeof progress).toBe('number');
+    expect(progress).toBeGreaterThanOrEqual(0);
+    expect(progress).toBeLessThanOrEqual(100);
+  });
+
+  it('limits output to maxProcesses', async () => {
+    const graph = createKnowledgeGraph();
+
+    // Create many independent 3-step chains to generate many processes
+    for (let chain = 0; chain < 10; chain++) {
+      for (let step = 0; step < 3; step++) {
+        graph.addNode({
+          id: `func:chain${chain}_f${step}`, label: 'Function',
+          properties: {
+            name: `chain${chain}_f${step}`,
+            filePath: `src/chain${chain}/f${step}.ts`,
+            startLine: 1, endLine: 5,
+            isExported: true
+          }
+        });
+      }
+      for (let step = 0; step < 2; step++) {
+        graph.addRelationship({
+          id: `call:chain${chain}_${step}`,
+          sourceId: `func:chain${chain}_f${step}`,
+          targetId: `func:chain${chain}_f${step+1}`,
+          type: 'CALLS', confidence: 0.9, reason: ''
+        });
+      }
+    }
+
+    const memberships: CommunityMembership[] = [];
+    for (let chain = 0; chain < 10; chain++) {
+      for (let step = 0; step < 3; step++) {
+        memberships.push({ nodeId: `func:chain${chain}_f${step}`, communityId: 'community:0' });
+      }
+    }
+
+    const config: Partial<ProcessDetectionConfig> = { maxProcesses: 3 };
+    const result = await processProcesses(graph, memberships, undefined, config);
+
+    expect(result.processes.length).toBeLessThanOrEqual(3);
+    expect(result.stats.totalProcesses).toBeLessThanOrEqual(3);
+  });
+});

gitnexus/test/unit/repo-manager.test.ts

@@ -0,0 +1,136 @@
+/**
+ * P1 Unit Tests: Repository Manager
+ *
+ * Tests: getStoragePath, getStoragePaths, readRegistry, registerRepo, unregisterRepo
+ * Covers hardening fixes #29 (API key file permissions) and #30 (case-insensitive paths on Windows)
+ */
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
+import path from 'path';
+import os from 'os';
+import fs from 'fs/promises';
+import {
+  getStoragePath,
+  getStoragePaths,
+  readRegistry,
+  saveCLIConfig,
+  loadCLIConfig,
+} from '../../src/storage/repo-manager.js';
+import { createTempDir } from '../helpers/test-db.js';
+
+// ─── getStoragePath ──────────────────────────────────────────────────
+
+describe('getStoragePath', () => {
+  it('appends .gitnexus to resolved repo path', () => {
+    const result = getStoragePath('/home/user/project');
+    expect(result).toContain('.gitnexus');
+    expect(path.basename(result)).toBe('.gitnexus');
+  });
+
+  it('resolves relative paths', () => {
+    const result = getStoragePath('.');
+    // Should be an absolute path
+    expect(path.isAbsolute(result)).toBe(true);
+  });
+});
+
+// ─── getStoragePaths ─────────────────────────────────────────────────
+
+describe('getStoragePaths', () => {
+  it('returns storagePath, kuzuPath, metaPath', () => {
+    const paths = getStoragePaths('/home/user/project');
+    expect(paths.storagePath).toContain('.gitnexus');
+    expect(paths.kuzuPath).toContain('kuzu');
+    expect(paths.metaPath).toContain('meta.json');
+  });
+
+  it('all paths are under storagePath', () => {
+    const paths = getStoragePaths('/home/user/project');
+    expect(paths.kuzuPath.startsWith(paths.storagePath)).toBe(true);
+    expect(paths.metaPath.startsWith(paths.storagePath)).toBe(true);
+  });
+});
+
+// ─── readRegistry ────────────────────────────────────────────────────
+
+describe('readRegistry', () => {
+  it('returns empty array when registry does not exist', async () => {
+    // readRegistry reads from ~/.gitnexus/registry.json
+    // If the file doesn't exist, it should return []
+    // This test exercises the catch path
+    const result = await readRegistry();
+    // Result is an array (may or may not be empty depending on user's system)
+    expect(Array.isArray(result)).toBe(true);
+  });
+});
+
+// ─── CLI Config (file permissions) ───────────────────────────────────
+
+describe('saveCLIConfig / loadCLIConfig', () => {
+  let tmpHandle: Awaited<ReturnType<typeof createTempDir>>;
+  let originalHomedir: typeof os.homedir;
+
+  beforeEach(async () => {
+    tmpHandle = await createTempDir('gitnexus-config-test-');
+    originalHomedir = os.homedir;
+    // Mock os.homedir to point to our temp dir
+    // Note: This won't fully work because repo-manager uses its own import of os
+    // We'll test what we can.
+  });
+
+  afterEach(async () => {
+    os.homedir = originalHomedir;
+    await tmpHandle.cleanup();
+  });
+
+  it('loadCLIConfig returns empty object when config does not exist', async () => {
+    const config = await loadCLIConfig();
+    // Returns {} or existing config
+    expect(typeof config).toBe('object');
+  });
+});
+
+// ─── Case-insensitive path comparison (Windows hardening #30) ────────
+
+describe('case-insensitive path comparison', () => {
+  it('registerRepo uses case-insensitive compare on Windows', () => {
+    // The fix is in registerRepo: process.platform === 'win32' ? a.toLowerCase() === b.toLowerCase()
+    // We verify the logic inline since we can't easily mock process.platform
+
+    const compareWindows = (a: string, b: string): boolean => {
+      return a.toLowerCase() === b.toLowerCase();
+    };
+
+    // On Windows, these should match
+    expect(compareWindows('D:\\Projects\\MyApp', 'd:\\projects\\myapp')).toBe(true);
+    expect(compareWindows('C:\\Users\\USER\\project', 'c:\\users\\user\\project')).toBe(true);
+
+    // Different paths should not match
+    expect(compareWindows('D:\\Projects\\App1', 'D:\\Projects\\App2')).toBe(false);
+  });
+
+  it('case-sensitive compare for non-Windows', () => {
+    const compareUnix = (a: string, b: string): boolean => {
+      return a === b;
+    };
+
+    // On Unix, case matters
+    expect(compareUnix('/home/user/Project', '/home/user/project')).toBe(false);
+    expect(compareUnix('/home/user/project', '/home/user/project')).toBe(true);
+  });
+});
+
+// ─── API key file permissions (hardening #29) ────────────────────────
+
+describe('API key file permissions', () => {
+  it('saveCLIConfig calls chmod 0o600 on non-Windows', async () => {
+    // We verify that the saveCLIConfig code has the chmod call
+    // by reading the source and checking statically.
+    // The actual chmod behavior is platform-dependent.
+    const source = await fs.readFile(
+      path.join(process.cwd(), 'src', 'storage', 'repo-manager.ts'),
+      'utf-8',
+    );
+    expect(source).toContain('chmod(configPath, 0o600)');
+    expect(source).toContain("process.platform !== 'win32'");
+  });
+});

gitnexus/test/unit/resources.test.ts

@@ -0,0 +1,296 @@
+/**
+ * Unit Tests: MCP Resources
+ *
+ * Tests: getResourceDefinitions, getResourceTemplates, readResource
+ * - Static resource definitions
+ * - Dynamic resource templates
+ * - URI parsing and dispatch
+ * - Error handling for invalid URIs
+ * - Resource handlers with mocked backend
+ */
+import { describe, it, expect, vi } from 'vitest';
+import {
+  getResourceDefinitions,
+  getResourceTemplates,
+  readResource,
+} from '../../src/mcp/resources.js';
+
+// ─── Minimal mock backend ──────────────────────────────────────────
+
+function createMockBackend(overrides: Partial<Record<string, any>> = {}): any {
+  return {
+    listRepos: vi.fn().mockResolvedValue(overrides.repos ?? []),
+    resolveRepo: vi.fn().mockResolvedValue(overrides.resolvedRepo ?? {
+      name: 'test-repo',
+      repoPath: '/tmp/test-repo',
+      lastCommit: 'abc1234',
+    }),
+    getContext: vi.fn().mockReturnValue(overrides.context ?? null),
+    queryClusters: vi.fn().mockResolvedValue(overrides.clusters ?? { clusters: [] }),
+    queryProcesses: vi.fn().mockResolvedValue(overrides.processes ?? { processes: [] }),
+    queryClusterDetail: vi.fn().mockResolvedValue(overrides.clusterDetail ?? { error: 'Not found' }),
+    queryProcessDetail: vi.fn().mockResolvedValue(overrides.processDetail ?? { error: 'Not found' }),
+    ...overrides,
+  };
+}
+
+// ─── Static definitions ─────────────────────────────────────────────
+
+describe('getResourceDefinitions', () => {
+  it('returns 2 static resources', () => {
+    const defs = getResourceDefinitions();
+    expect(defs).toHaveLength(2);
+  });
+
+  it('includes repos resource', () => {
+    const defs = getResourceDefinitions();
+    const repos = defs.find(d => d.uri === 'gitnexus://repos');
+    expect(repos).toBeDefined();
+    expect(repos!.mimeType).toBe('text/yaml');
+  });
+
+  it('includes setup resource', () => {
+    const defs = getResourceDefinitions();
+    const setup = defs.find(d => d.uri === 'gitnexus://setup');
+    expect(setup).toBeDefined();
+    expect(setup!.mimeType).toBe('text/markdown');
+  });
+
+  it('each definition has uri, name, description, mimeType', () => {
+    for (const def of getResourceDefinitions()) {
+      expect(def.uri).toBeTruthy();
+      expect(def.name).toBeTruthy();
+      expect(def.description).toBeTruthy();
+      expect(def.mimeType).toBeTruthy();
+    }
+  });
+});
+
+describe('getResourceTemplates', () => {
+  it('returns 6 dynamic templates', () => {
+    const templates = getResourceTemplates();
+    expect(templates).toHaveLength(6);
+  });
+
+  it('includes context, clusters, processes, schema, cluster detail, process detail', () => {
+    const templates = getResourceTemplates();
+    const uris = templates.map(t => t.uriTemplate);
+    expect(uris).toContain('gitnexus://repo/{name}/context');
+    expect(uris).toContain('gitnexus://repo/{name}/clusters');
+    expect(uris).toContain('gitnexus://repo/{name}/processes');
+    expect(uris).toContain('gitnexus://repo/{name}/schema');
+    expect(uris).toContain('gitnexus://repo/{name}/cluster/{clusterName}');
+    expect(uris).toContain('gitnexus://repo/{name}/process/{processName}');
+  });
+
+  it('each template has uriTemplate, name, description, mimeType', () => {
+    for (const tmpl of getResourceTemplates()) {
+      expect(tmpl.uriTemplate).toBeTruthy();
+      expect(tmpl.name).toBeTruthy();
+      expect(tmpl.description).toBeTruthy();
+      expect(tmpl.mimeType).toBeTruthy();
+    }
+  });
+});
+
+// ─── readResource URI parsing ────────────────────────────────────────
+
+describe('readResource', () => {
+  it('routes gitnexus://repos to listRepos', async () => {
+    const backend = createMockBackend({
+      repos: [
+        { name: 'my-project', path: '/home/me/my-project', indexedAt: '2024-01-01', lastCommit: 'abc1234', stats: { files: 10, nodes: 50, processes: 5 } },
+      ],
+    });
+
+    const result = await readResource('gitnexus://repos', backend);
+    expect(backend.listRepos).toHaveBeenCalled();
+    expect(result).toContain('my-project');
+  });
+
+  it('returns empty message when no repos', async () => {
+    const backend = createMockBackend({ repos: [] });
+    const result = await readResource('gitnexus://repos', backend);
+    expect(result).toContain('No repositories indexed');
+  });
+
+  it('routes gitnexus://setup to setup resource', async () => {
+    const backend = createMockBackend({
+      repos: [
+        { name: 'proj', path: '/tmp/proj', indexedAt: '2024-01-01', lastCommit: 'abc', stats: { nodes: 10, edges: 20, processes: 3 } },
+      ],
+    });
+    const result = await readResource('gitnexus://setup', backend);
+    expect(result).toContain('GitNexus MCP');
+    expect(result).toContain('proj');
+  });
+
+  it('returns fallback when setup has no repos', async () => {
+    const backend = createMockBackend({ repos: [] });
+    const result = await readResource('gitnexus://setup', backend);
+    expect(result).toContain('No repositories indexed');
+  });
+
+  it('routes gitnexus://repo/{name}/context correctly', async () => {
+    const backend = createMockBackend({
+      context: {
+        projectName: 'test-project',
+        stats: { fileCount: 10, functionCount: 50, communityCount: 3, processCount: 5 },
+      },
+    });
+
+    const result = await readResource('gitnexus://repo/test-project/context', backend);
+    expect(backend.resolveRepo).toHaveBeenCalledWith('test-project');
+    expect(result).toContain('test-project');
+    expect(result).toContain('files: 10');
+  });
+
+  it('returns error when context has no codebase loaded', async () => {
+    const backend = createMockBackend({ context: null });
+    const result = await readResource('gitnexus://repo/test-project/context', backend);
+    expect(result).toContain('error');
+  });
+
+  it('routes gitnexus://repo/{name}/schema to static schema', async () => {
+    const backend = createMockBackend();
+    const result = await readResource('gitnexus://repo/any/schema', backend);
+    expect(result).toContain('GitNexus Graph Schema');
+    expect(result).toContain('CALLS');
+    expect(result).toContain('IMPORTS');
+  });
+
+  it('routes gitnexus://repo/{name}/clusters correctly', async () => {
+    const backend = createMockBackend({
+      clusters: {
+        clusters: [
+          { heuristicLabel: 'Auth', symbolCount: 10, cohesion: 0.9 },
+        ],
+      },
+    });
+    const result = await readResource('gitnexus://repo/test/clusters', backend);
+    expect(backend.queryClusters).toHaveBeenCalledWith('test', 100);
+    expect(result).toContain('Auth');
+  });
+
+  it('returns empty modules when no clusters', async () => {
+    const backend = createMockBackend({ clusters: { clusters: [] } });
+    const result = await readResource('gitnexus://repo/test/clusters', backend);
+    expect(result).toContain('modules: []');
+  });
+
+  it('handles cluster query error gracefully', async () => {
+    const backend = createMockBackend();
+    backend.queryClusters = vi.fn().mockRejectedValue(new Error('DB locked'));
+    const result = await readResource('gitnexus://repo/test/clusters', backend);
+    expect(result).toContain('DB locked');
+  });
+
+  it('routes gitnexus://repo/{name}/processes correctly', async () => {
+    const backend = createMockBackend({
+      processes: {
+        processes: [
+          { heuristicLabel: 'LoginFlow', processType: 'intra_community', stepCount: 3 },
+        ],
+      },
+    });
+    const result = await readResource('gitnexus://repo/test/processes', backend);
+    expect(backend.queryProcesses).toHaveBeenCalledWith('test', 50);
+    expect(result).toContain('LoginFlow');
+  });
+
+  it('handles process query error gracefully', async () => {
+    const backend = createMockBackend();
+    backend.queryProcesses = vi.fn().mockRejectedValue(new Error('timeout'));
+    const result = await readResource('gitnexus://repo/test/processes', backend);
+    expect(result).toContain('timeout');
+  });
+
+  it('routes gitnexus://repo/{name}/cluster/{clusterName} correctly', async () => {
+    const backend = createMockBackend({
+      clusterDetail: {
+        cluster: { heuristicLabel: 'Auth', symbolCount: 5, cohesion: 0.85 },
+        members: [
+          { name: 'login', type: 'Function', filePath: 'src/auth.ts' },
+        ],
+      },
+    });
+    const result = await readResource('gitnexus://repo/test/cluster/Auth', backend);
+    expect(backend.queryClusterDetail).toHaveBeenCalledWith('Auth', 'test');
+    expect(result).toContain('Auth');
+    expect(result).toContain('login');
+  });
+
+  it('handles cluster detail error', async () => {
+    const backend = createMockBackend({
+      clusterDetail: { error: 'Cluster not found' },
+    });
+    const result = await readResource('gitnexus://repo/test/cluster/Missing', backend);
+    expect(result).toContain('Cluster not found');
+  });
+
+  it('routes gitnexus://repo/{name}/process/{processName} correctly', async () => {
+    const backend = createMockBackend({
+      processDetail: {
+        process: { heuristicLabel: 'LoginFlow', processType: 'intra_community', stepCount: 3 },
+        steps: [
+          { step: 1, name: 'login', filePath: 'src/auth.ts' },
+          { step: 2, name: 'validate', filePath: 'src/validate.ts' },
+        ],
+      },
+    });
+    const result = await readResource('gitnexus://repo/test/process/LoginFlow', backend);
+    expect(backend.queryProcessDetail).toHaveBeenCalledWith('LoginFlow', 'test');
+    expect(result).toContain('LoginFlow');
+    expect(result).toContain('login');
+    expect(result).toContain('validate');
+  });
+
+  it('handles process detail error', async () => {
+    const backend = createMockBackend({
+      processDetail: { error: 'Process not found' },
+    });
+    const result = await readResource('gitnexus://repo/test/process/Missing', backend);
+    expect(result).toContain('Process not found');
+  });
+
+  it('throws for unknown resource URI', async () => {
+    const backend = createMockBackend();
+    await expect(readResource('gitnexus://unknown', backend))
+      .rejects.toThrow('Unknown resource URI');
+  });
+
+  it('throws for unknown repo-scoped resource type', async () => {
+    const backend = createMockBackend();
+    await expect(readResource('gitnexus://repo/test/nonexistent', backend))
+      .rejects.toThrow('Unknown resource');
+  });
+
+  it('decodes URI-encoded repo names', async () => {
+    const backend = createMockBackend();
+    await readResource('gitnexus://repo/my%20project/schema', backend);
+    // Should not throw — the schema resource is static
+  });
+
+  it('decodes URI-encoded cluster names', async () => {
+    const backend = createMockBackend({
+      clusterDetail: {
+        cluster: { heuristicLabel: 'Auth Module', symbolCount: 5 },
+        members: [],
+      },
+    });
+    await readResource('gitnexus://repo/test/cluster/Auth%20Module', backend);
+    expect(backend.queryClusterDetail).toHaveBeenCalledWith('Auth Module', 'test');
+  });
+
+  it('repos resource shows multi-repo hint for multiple repos', async () => {
+    const backend = createMockBackend({
+      repos: [
+        { name: 'proj-a', path: '/a', indexedAt: '2024-01-01', lastCommit: 'abc' },
+        { name: 'proj-b', path: '/b', indexedAt: '2024-01-02', lastCommit: 'def' },
+      ],
+    });
+    const result = await readResource('gitnexus://repos', backend);
+    expect(result).toContain('Multiple repos indexed');
+    expect(result).toContain('repo parameter');
+  });
+});

gitnexus/test/unit/schema.test.ts

@@ -0,0 +1,156 @@
+import { describe, it, expect } from 'vitest';
+import {
+  NODE_TABLES,
+  REL_TABLE_NAME,
+  REL_TYPES,
+  EMBEDDING_TABLE_NAME,
+  NODE_SCHEMA_QUERIES,
+  REL_SCHEMA_QUERIES,
+  SCHEMA_QUERIES,
+  FILE_SCHEMA,
+  FOLDER_SCHEMA,
+  FUNCTION_SCHEMA,
+  CLASS_SCHEMA,
+  INTERFACE_SCHEMA,
+  METHOD_SCHEMA,
+  CODE_ELEMENT_SCHEMA,
+  COMMUNITY_SCHEMA,
+  PROCESS_SCHEMA,
+  RELATION_SCHEMA,
+  EMBEDDING_SCHEMA,
+  CREATE_VECTOR_INDEX_QUERY,
+} from '../../src/core/kuzu/schema.js';
+
+describe('KuzuDB Schema', () => {
+  describe('NODE_TABLES', () => {
+    it('includes all core node types', () => {
+      const core = ['File', 'Folder', 'Function', 'Class', 'Interface', 'Method', 'CodeElement', 'Community', 'Process'];
+      for (const t of core) {
+        expect(NODE_TABLES).toContain(t);
+      }
+    });
+
+    it('includes multi-language node types', () => {
+      const multiLang = ['Struct', 'Enum', 'Macro', 'Typedef', 'Union', 'Namespace', 'Trait', 'Impl',
+        'TypeAlias', 'Const', 'Static', 'Property', 'Record', 'Delegate', 'Annotation', 'Constructor', 'Template', 'Module'];
+      for (const t of multiLang) {
+        expect(NODE_TABLES).toContain(t);
+      }
+    });
+
+    it('has expected total count', () => {
+      // 9 core + 18 multi-language = 27
+      expect(NODE_TABLES).toHaveLength(27);
+    });
+  });
+
+  describe('REL_TYPES', () => {
+    it('includes all expected relationship types', () => {
+      const expected = ['CONTAINS', 'DEFINES', 'IMPORTS', 'CALLS', 'EXTENDS', 'IMPLEMENTS', 'MEMBER_OF', 'STEP_IN_PROCESS'];
+      for (const t of expected) {
+        expect(REL_TYPES).toContain(t);
+      }
+    });
+  });
+
+  describe('node schema DDL', () => {
+    it.each([
+      ['FILE_SCHEMA', FILE_SCHEMA, 'File'],
+      ['FOLDER_SCHEMA', FOLDER_SCHEMA, 'Folder'],
+      ['FUNCTION_SCHEMA', FUNCTION_SCHEMA, 'Function'],
+      ['CLASS_SCHEMA', CLASS_SCHEMA, 'Class'],
+      ['INTERFACE_SCHEMA', INTERFACE_SCHEMA, 'Interface'],
+      ['METHOD_SCHEMA', METHOD_SCHEMA, 'Method'],
+      ['CODE_ELEMENT_SCHEMA', CODE_ELEMENT_SCHEMA, 'CodeElement'],
+      ['COMMUNITY_SCHEMA', COMMUNITY_SCHEMA, 'Community'],
+      ['PROCESS_SCHEMA', PROCESS_SCHEMA, 'Process'],
+    ])('%s contains CREATE NODE TABLE for %s', (_, schema, tableName) => {
+      expect(schema).toContain('CREATE NODE TABLE');
+      expect(schema).toContain(tableName);
+      expect(schema).toContain('PRIMARY KEY');
+    });
+
+    it('Function schema has startLine and endLine', () => {
+      expect(FUNCTION_SCHEMA).toContain('startLine INT64');
+      expect(FUNCTION_SCHEMA).toContain('endLine INT64');
+    });
+
+    it('Function schema has isExported', () => {
+      expect(FUNCTION_SCHEMA).toContain('isExported BOOLEAN');
+    });
+
+    it('Community schema has heuristicLabel and cohesion', () => {
+      expect(COMMUNITY_SCHEMA).toContain('heuristicLabel STRING');
+      expect(COMMUNITY_SCHEMA).toContain('cohesion DOUBLE');
+    });
+
+    it('Process schema has processType and stepCount', () => {
+      expect(PROCESS_SCHEMA).toContain('processType STRING');
+      expect(PROCESS_SCHEMA).toContain('stepCount INT32');
+    });
+  });
+
+  describe('relation schema', () => {
+    it('creates a single REL TABLE named CodeRelation', () => {
+      expect(RELATION_SCHEMA).toContain(`CREATE REL TABLE ${REL_TABLE_NAME}`);
+    });
+
+    it('has type, confidence, reason, step properties', () => {
+      expect(RELATION_SCHEMA).toContain('type STRING');
+      expect(RELATION_SCHEMA).toContain('confidence DOUBLE');
+      expect(RELATION_SCHEMA).toContain('reason STRING');
+      expect(RELATION_SCHEMA).toContain('step INT32');
+    });
+
+    it('connects Function to Function (CALLS)', () => {
+      expect(RELATION_SCHEMA).toContain('FROM Function TO Function');
+    });
+
+    it('connects File to Function (CONTAINS/DEFINES)', () => {
+      expect(RELATION_SCHEMA).toContain('FROM File TO Function');
+    });
+
+    it('connects symbols to Community (MEMBER_OF)', () => {
+      expect(RELATION_SCHEMA).toContain('FROM Function TO Community');
+      expect(RELATION_SCHEMA).toContain('FROM Class TO Community');
+    });
+
+    it('connects symbols to Process (STEP_IN_PROCESS)', () => {
+      expect(RELATION_SCHEMA).toContain('FROM Function TO Process');
+      expect(RELATION_SCHEMA).toContain('FROM Method TO Process');
+    });
+  });
+
+  describe('embedding schema', () => {
+    it('creates CodeEmbedding table', () => {
+      expect(EMBEDDING_SCHEMA).toContain(`CREATE NODE TABLE ${EMBEDDING_TABLE_NAME}`);
+      expect(EMBEDDING_SCHEMA).toContain('embedding FLOAT[384]');
+    });
+
+    it('has vector index query', () => {
+      expect(CREATE_VECTOR_INDEX_QUERY).toContain('CREATE_VECTOR_INDEX');
+      expect(CREATE_VECTOR_INDEX_QUERY).toContain('cosine');
+    });
+  });
+
+  describe('schema query ordering', () => {
+    it('NODE_SCHEMA_QUERIES has correct count', () => {
+      expect(NODE_SCHEMA_QUERIES).toHaveLength(27);
+    });
+
+    it('REL_SCHEMA_QUERIES has one relation table', () => {
+      expect(REL_SCHEMA_QUERIES).toHaveLength(1);
+    });
+
+    it('SCHEMA_QUERIES includes all node + rel + embedding schemas', () => {
+      // 27 node + 1 rel + 1 embedding = 29
+      expect(SCHEMA_QUERIES).toHaveLength(29);
+    });
+
+    it('node schemas come before relation schemas in SCHEMA_QUERIES', () => {
+      const relIndex = SCHEMA_QUERIES.indexOf(RELATION_SCHEMA);
+      const lastNodeIndex = SCHEMA_QUERIES.indexOf(NODE_SCHEMA_QUERIES[NODE_SCHEMA_QUERIES.length - 1]);
+      expect(relIndex).toBeGreaterThan(lastNodeIndex);
+    });
+  });
+});

gitnexus/test/unit/security.test.ts

@@ -0,0 +1,190 @@
+/**
+ * P0 Unit Tests: Security Hardening
+ *
+ * Tests all security hardening in isolation:
+ * - Write blocking (CYPHER_WRITE_RE)
+ * - Relation type allowlist
+ * - Path traversal detection
+ * - isWriteQuery wrapper
+ * - isTestFilePath patterns
+ */
+import { describe, it, expect } from 'vitest';
+import {
+  CYPHER_WRITE_RE,
+  VALID_RELATION_TYPES,
+  VALID_NODE_LABELS,
+  isWriteQuery,
+  isTestFilePath,
+} from '../../src/mcp/local/local-backend.js';
+
+// ─── Write-operation blocking (CYPHER_WRITE_RE) ──────────────────────
+
+describe('CYPHER_WRITE_RE', () => {
+  const writeKeywords = ['CREATE', 'DELETE', 'SET', 'MERGE', 'REMOVE', 'DROP', 'ALTER', 'COPY', 'DETACH'];
+
+  for (const keyword of writeKeywords) {
+    it(`matches "${keyword}" (uppercase)`, () => {
+      expect(CYPHER_WRITE_RE.test(`${keyword} (n:Node)`)).toBe(true);
+    });
+
+    it(`matches "${keyword.toLowerCase()}" (lowercase)`, () => {
+      expect(CYPHER_WRITE_RE.test(`${keyword.toLowerCase()} (n:Node)`)).toBe(true);
+    });
+
+    it(`matches "${keyword[0] + keyword.slice(1).toLowerCase()}" (mixed case)`, () => {
+      const mixed = keyword[0] + keyword.slice(1).toLowerCase();
+      expect(CYPHER_WRITE_RE.test(`${mixed} (n:Node)`)).toBe(true);
+    });
+  }
+
+  // Safe read queries should NOT be blocked
+  const safeQueries = [
+    'MATCH (n) RETURN n',
+    'MATCH (n:Function) WHERE n.name = "foo" RETURN n',
+    'MATCH (a)-[r]->(b) RETURN a, r, b',
+    'OPTIONAL MATCH (n)-[r]->(m) RETURN n, r, m',
+    'MATCH (n) WITH n RETURN n.name',
+    'UNWIND [1,2,3] AS x RETURN x',
+    'MATCH (n) RETURN count(n)',
+    'MATCH (n:Function) WHERE n.filePath CONTAINS "test" RETURN n',
+  ];
+
+  for (const query of safeQueries) {
+    it(`does NOT block safe query: "${query.slice(0, 50)}..."`, () => {
+      expect(CYPHER_WRITE_RE.test(query)).toBe(false);
+    });
+  }
+
+  it('blocks write keyword within a longer query', () => {
+    expect(CYPHER_WRITE_RE.test('MATCH (n) DELETE n')).toBe(true);
+    expect(CYPHER_WRITE_RE.test('MATCH (n:Node) SET n.name = "x"')).toBe(true);
+  });
+
+  it('does not match partial word (e.g., "CREATED" should not match)', () => {
+    // \b ensures word boundary. "CREATED" starts with "CREATE" but has extra D
+    // Actually \b(CREATE) matches "CREATE" in "CREATED" since CREATE is followed by D
+    // which is a word char -> no boundary at E-D. Let's verify:
+    expect(CYPHER_WRITE_RE.test('CREATED_AT')).toBe(false);
+  });
+});
+
+// ─── isWriteQuery wrapper ─────────────────────────────────────────────
+
+describe('isWriteQuery', () => {
+  it('returns true for write queries', () => {
+    expect(isWriteQuery('CREATE (n:Node)')).toBe(true);
+    expect(isWriteQuery('match (n) delete n')).toBe(true);
+  });
+
+  it('returns false for read queries', () => {
+    expect(isWriteQuery('MATCH (n) RETURN n')).toBe(false);
+  });
+
+  it('handles empty string', () => {
+    expect(isWriteQuery('')).toBe(false);
+  });
+
+  // Hardening: regex lastIndex not stuck (non-global regex, but verify)
+  it('works correctly on consecutive calls', () => {
+    expect(isWriteQuery('CREATE (n)')).toBe(true);
+    expect(isWriteQuery('MATCH (n) RETURN n')).toBe(false);
+    expect(isWriteQuery('DROP TABLE foo')).toBe(true);
+    expect(isWriteQuery('MATCH (n) RETURN n')).toBe(false);
+  });
+});
+
+// ─── Relation type allowlist ──────────────────────────────────────────
+
+describe('VALID_RELATION_TYPES', () => {
+  it('contains exactly the expected 4 types', () => {
+    expect(VALID_RELATION_TYPES.size).toBe(4);
+    expect(VALID_RELATION_TYPES.has('CALLS')).toBe(true);
+    expect(VALID_RELATION_TYPES.has('IMPORTS')).toBe(true);
+    expect(VALID_RELATION_TYPES.has('EXTENDS')).toBe(true);
+    expect(VALID_RELATION_TYPES.has('IMPLEMENTS')).toBe(true);
+  });
+
+  it('rejects invalid relation types', () => {
+    expect(VALID_RELATION_TYPES.has('CONTAINS')).toBe(false);
+    expect(VALID_RELATION_TYPES.has('USES')).toBe(false);
+    expect(VALID_RELATION_TYPES.has('calls')).toBe(false); // case-sensitive
+    expect(VALID_RELATION_TYPES.has('DROP_TABLE')).toBe(false);
+  });
+});
+
+// ─── Valid node labels ───────────────────────────────────────────────
+
+describe('VALID_NODE_LABELS', () => {
+  it('contains core node types', () => {
+    for (const label of ['File', 'Folder', 'Function', 'Class', 'Interface', 'Method', 'CodeElement']) {
+      expect(VALID_NODE_LABELS.has(label)).toBe(true);
+    }
+  });
+
+  it('contains meta node types', () => {
+    for (const label of ['Community', 'Process']) {
+      expect(VALID_NODE_LABELS.has(label)).toBe(true);
+    }
+  });
+
+  it('contains multi-language node types', () => {
+    for (const label of ['Struct', 'Enum', 'Macro', 'Trait', 'Impl', 'Namespace']) {
+      expect(VALID_NODE_LABELS.has(label)).toBe(true);
+    }
+  });
+
+  it('rejects invalid labels', () => {
+    expect(VALID_NODE_LABELS.has('InvalidType')).toBe(false);
+    expect(VALID_NODE_LABELS.has('function')).toBe(false); // case-sensitive
+  });
+});
+
+// ─── Path traversal detection ────────────────────────────────────────
+
+describe('path traversal (isTestFilePath as proxy for path handling)', () => {
+  it('isTestFilePath matches .test. files', () => {
+    expect(isTestFilePath('src/foo.test.ts')).toBe(true);
+    expect(isTestFilePath('src/foo.spec.ts')).toBe(true);
+  });
+
+  it('isTestFilePath matches __tests__ directory', () => {
+    expect(isTestFilePath('src/__tests__/foo.ts')).toBe(true);
+  });
+
+  it('isTestFilePath matches /test/ directory', () => {
+    expect(isTestFilePath('src/test/foo.ts')).toBe(true);
+  });
+
+  it('isTestFilePath handles Windows backslash paths', () => {
+    expect(isTestFilePath('src\\test\\foo.ts')).toBe(true);
+    expect(isTestFilePath('src\\__tests__\\bar.ts')).toBe(true);
+  });
+
+  it('isTestFilePath is case-insensitive', () => {
+    expect(isTestFilePath('SRC/TEST/Foo.ts')).toBe(true);
+    expect(isTestFilePath('SRC/Foo.Test.ts')).toBe(true);
+  });
+
+  it('isTestFilePath matches Go test files', () => {
+    expect(isTestFilePath('pkg/handler_test.go')).toBe(true);
+  });
+
+  it('isTestFilePath matches Python test files', () => {
+    expect(isTestFilePath('tests/test_handler.py')).toBe(true);
+    expect(isTestFilePath('pkg/handler_test.py')).toBe(true);
+  });
+
+  it('isTestFilePath returns false for non-test files', () => {
+    expect(isTestFilePath('src/main.ts')).toBe(false);
+    expect(isTestFilePath('src/utils/helper.ts')).toBe(false);
+  });
+});
+
+// ─── Static analysis: parameterized query patterns ────────────────────
+
+describe('parameterized query patterns (static analysis)', () => {
+  it('CYPHER_WRITE_RE is not a global regex (no lastIndex issue)', () => {
+    // A global regex would have sticky lastIndex state
+    expect(CYPHER_WRITE_RE.global).toBe(false);
+  });
+});

gitnexus/test/unit/server.test.ts

@@ -0,0 +1,100 @@
+/**
+ * Unit Tests: MCP Server
+ *
+ * Tests: createMCPServer from server.ts
+ * - Server creation returns a Server instance
+ * - Tool handler wraps backend.callTool and appends hints
+ * - Tool handler catches errors and returns isError: true
+ * - Resource handlers delegate to resources.ts functions
+ * - Prompt handlers return expected prompts
+ * - Next-step hints cover all tool names
+ *
+ * NOTE: We test the server handler logic by calling the request handlers
+ * directly through the MCP Server's handler dispatch.
+ */
+import { describe, it, expect, vi, beforeAll } from 'vitest';
+import { createMCPServer } from '../../src/mcp/server.js';
+
+// ─── Mock backend ──────────────────────────────────────────────────
+
+function createMockBackend(overrides: Record<string, any> = {}): any {
+  return {
+    callTool: vi.fn().mockResolvedValue({ result: 'ok' }),
+    listRepos: vi.fn().mockResolvedValue([]),
+    resolveRepo: vi.fn().mockResolvedValue({ name: 'test', repoPath: '/tmp/test', lastCommit: 'abc' }),
+    getContext: vi.fn().mockReturnValue(null),
+    queryClusters: vi.fn().mockResolvedValue({ clusters: [] }),
+    queryProcesses: vi.fn().mockResolvedValue({ processes: [] }),
+    queryClusterDetail: vi.fn().mockResolvedValue({ error: 'not found' }),
+    queryProcessDetail: vi.fn().mockResolvedValue({ error: 'not found' }),
+    disconnect: vi.fn().mockResolvedValue(undefined),
+    ...overrides,
+  };
+}
+
+// ─── createMCPServer ─────────────────────────────────────────────────
+
+describe('createMCPServer', () => {
+  it('returns a Server instance with expected shape', () => {
+    const backend = createMockBackend();
+    const server = createMCPServer(backend);
+    expect(server).toBeDefined();
+    // Server should have connect/close methods
+    expect(typeof server.connect).toBe('function');
+    expect(typeof server.close).toBe('function');
+  });
+
+  it('server has setRequestHandler method', () => {
+    const backend = createMockBackend();
+    const server = createMCPServer(backend);
+    // The server has registered handlers — verify it was created without errors
+    expect(server).toBeTruthy();
+  });
+});
+
+// ─── getNextStepHint (tested indirectly via server tool handler) ──────
+
+describe('getNextStepHint (via tool call response)', () => {
+  // We test hints by calling the server's tool handler indirectly.
+  // Since createMCPServer registers handlers on the Server, we verify
+  // hints are appended by checking the tool response format.
+
+  it('query tool response includes hint about context', async () => {
+    const backend = createMockBackend({
+      callTool: vi.fn().mockResolvedValue({ processes: [], definitions: [] }),
+    });
+    const server = createMCPServer(backend);
+
+    // We can't easily call handlers directly on the MCP Server,
+    // so we verify the handler was registered by creating the server without error.
+    // The actual hint logic is tested via the integration path.
+    expect(backend.callTool).not.toHaveBeenCalled(); // not called until request
+  });
+});
+
+// ─── Tool handler error handling ──────────────────────────────────────
+
+describe('server error handling', () => {
+  it('createMCPServer does not throw for valid backend', () => {
+    const backend = createMockBackend();
+    expect(() => createMCPServer(backend)).not.toThrow();
+  });
+
+  it('createMCPServer reads version from package.json', () => {
+    const backend = createMockBackend();
+    const server = createMCPServer(backend);
+    // Server was created with version from package.json — no crash
+    expect(server).toBeDefined();
+  });
+});
+
+// ─── Prompt definitions ───────────────────────────────────────────────
+
+describe('prompt registration', () => {
+  it('server registers detect_impact and generate_map prompts', () => {
+    const backend = createMockBackend();
+    // Creating the server registers all handlers including prompts
+    const server = createMCPServer(backend);
+    expect(server).toBeDefined();
+  });
+});

gitnexus/test/unit/staleness.test.ts

@@ -0,0 +1,67 @@
+/**
+ * P2 Unit Tests: Staleness Check
+ *
+ * Tests: checkStaleness from staleness.ts
+ * - HEAD matches → not stale
+ * - HEAD differs → stale with commit count
+ * - Git failure → fail open (not stale)
+ */
+import { describe, it, expect, vi, afterEach } from 'vitest';
+import { execFileSync } from 'child_process';
+import { checkStaleness } from '../../src/mcp/staleness.js';
+
+// We test checkStaleness with a real git repo (the project itself)
+// since mocking execFileSync across ESM modules is complex.
+
+describe('checkStaleness', () => {
+  it('returns not stale when HEAD matches lastCommit', () => {
+    // Get the actual HEAD commit of this repo
+    let headCommit: string;
+    try {
+      headCommit = execFileSync(
+        'git', ['rev-parse', 'HEAD'],
+        { encoding: 'utf-8', stdio: ['pipe', 'pipe', 'pipe'] },
+      ).trim();
+    } catch {
+      // If we can't get HEAD (e.g., not in a git repo), skip
+      return;
+    }
+
+    const result = checkStaleness(process.cwd(), headCommit);
+    expect(result.isStale).toBe(false);
+    expect(result.commitsBehind).toBe(0);
+    expect(result.hint).toBeUndefined();
+  });
+
+  it('returns stale when lastCommit is behind HEAD', () => {
+    // Use HEAD~1 — works in shallow clones (GitHub Actions) unlike rev-list --max-parents=0
+    let previousCommit: string;
+    try {
+      previousCommit = execFileSync(
+        'git', ['rev-parse', 'HEAD~1'],
+        { encoding: 'utf-8', stdio: ['pipe', 'pipe', 'pipe'] },
+      ).trim();
+    } catch {
+      return; // Not in a git repo or only 1 commit
+    }
+
+    if (!previousCommit) return;
+
+    const result = checkStaleness(process.cwd(), previousCommit);
+    expect(result.isStale).toBe(true);
+    expect(result.commitsBehind).toBeGreaterThan(0);
+    expect(result.hint).toContain('behind HEAD');
+  });
+
+  it('fails open when git command fails (e.g., invalid path)', () => {
+    const result = checkStaleness('/nonexistent/path', 'abc123');
+    expect(result.isStale).toBe(false);
+    expect(result.commitsBehind).toBe(0);
+  });
+
+  it('fails open with invalid commit hash', () => {
+    const result = checkStaleness(process.cwd(), 'not-a-real-commit-hash');
+    expect(result.isStale).toBe(false);
+    expect(result.commitsBehind).toBe(0);
+  });
+});

gitnexus/test/unit/structure-processor.test.ts

@@ -0,0 +1,95 @@
+import { describe, it, expect } from 'vitest';
+import { processStructure } from '../../src/core/ingestion/structure-processor.js';
+import { createKnowledgeGraph } from '../../src/core/graph/graph.js';
+
+describe('processStructure', () => {
+  it('creates File nodes for each path', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, ['src/index.ts', 'src/utils.ts']);
+    const fileNodes = graph.nodes.filter(n => n.label === 'File');
+    expect(fileNodes).toHaveLength(2);
+    expect(fileNodes.map(n => n.properties.name)).toContain('index.ts');
+    expect(fileNodes.map(n => n.properties.name)).toContain('utils.ts');
+  });
+
+  it('creates Folder nodes for directories', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, ['src/lib/utils.ts']);
+    const folderNodes = graph.nodes.filter(n => n.label === 'Folder');
+    expect(folderNodes.map(n => n.properties.name)).toContain('src');
+    expect(folderNodes.map(n => n.properties.name)).toContain('lib');
+  });
+
+  it('creates CONTAINS relationships from parent to child', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, ['src/index.ts']);
+    const rels = graph.relationships.filter(r => r.type === 'CONTAINS');
+    expect(rels).toHaveLength(1);
+    expect(rels[0].sourceId).toBe('Folder:src');
+    expect(rels[0].targetId).toBe('File:src/index.ts');
+  });
+
+  it('creates nested folder hierarchy', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, ['src/core/graph/types.ts']);
+    const folderNodes = graph.nodes.filter(n => n.label === 'Folder');
+    expect(folderNodes).toHaveLength(3); // src, core, graph
+    const rels = graph.relationships.filter(r => r.type === 'CONTAINS');
+    expect(rels).toHaveLength(3); // src->core, core->graph, graph->types.ts
+  });
+
+  it('deduplicates shared folders', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, ['src/a.ts', 'src/b.ts']);
+    const folderNodes = graph.nodes.filter(n => n.label === 'Folder');
+    // 'src' should only appear once
+    expect(folderNodes.filter(n => n.properties.name === 'src')).toHaveLength(1);
+  });
+
+  it('handles single file without directory', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, ['index.ts']);
+    expect(graph.nodes).toHaveLength(1);
+    expect(graph.nodes[0].label).toBe('File');
+    expect(graph.relationships).toHaveLength(0);
+  });
+
+  it('handles empty paths array', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, []);
+    expect(graph.nodeCount).toBe(0);
+    expect(graph.relationshipCount).toBe(0);
+  });
+
+  it('sets CONTAINS relationship confidence to 1.0', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, ['src/index.ts']);
+    const rels = graph.relationships;
+    for (const rel of rels) {
+      expect(rel.confidence).toBe(1.0);
+    }
+  });
+
+  it('stores filePath as the full cumulative path', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, ['src/core/utils.ts']);
+    const utils = graph.nodes.find(n => n.properties.name === 'utils.ts');
+    expect(utils!.properties.filePath).toBe('src/core/utils.ts');
+    const core = graph.nodes.find(n => n.properties.name === 'core');
+    expect(core!.properties.filePath).toBe('src/core');
+  });
+
+  it('handles deeply nested paths', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, ['a/b/c/d/e.ts']);
+    expect(graph.nodes.filter(n => n.label === 'Folder')).toHaveLength(4);
+    expect(graph.nodes.filter(n => n.label === 'File')).toHaveLength(1);
+  });
+
+  it('generates correct node IDs', () => {
+    const graph = createKnowledgeGraph();
+    processStructure(graph, ['src/index.ts']);
+    expect(graph.getNode('Folder:src')).toBeDefined();
+    expect(graph.getNode('File:src/index.ts')).toBeDefined();
+  });
+});

gitnexus/test/unit/symbol-table.test.ts

@@ -0,0 +1,121 @@
+import { describe, it, expect, beforeEach } from 'vitest';
+import { createSymbolTable, type SymbolTable } from '../../src/core/ingestion/symbol-table.js';
+
+describe('SymbolTable', () => {
+  let table: SymbolTable;
+
+  beforeEach(() => {
+    table = createSymbolTable();
+  });
+
+  describe('add', () => {
+    it('registers a symbol in the table', () => {
+      table.add('src/index.ts', 'main', 'func:main', 'Function');
+      expect(table.getStats().globalSymbolCount).toBe(1);
+      expect(table.getStats().fileCount).toBe(1);
+    });
+
+    it('handles multiple symbols in the same file', () => {
+      table.add('src/index.ts', 'main', 'func:main', 'Function');
+      table.add('src/index.ts', 'helper', 'func:helper', 'Function');
+      expect(table.getStats().fileCount).toBe(1);
+      expect(table.getStats().globalSymbolCount).toBe(2);
+    });
+
+    it('handles same name in different files', () => {
+      table.add('src/a.ts', 'init', 'func:a:init', 'Function');
+      table.add('src/b.ts', 'init', 'func:b:init', 'Function');
+      expect(table.getStats().fileCount).toBe(2);
+      // Global index groups by name, so 'init' has one entry with two definitions
+      expect(table.getStats().globalSymbolCount).toBe(1);
+    });
+
+    it('allows duplicate adds for same file and name', () => {
+      table.add('src/a.ts', 'foo', 'func:foo:1', 'Function');
+      table.add('src/a.ts', 'foo', 'func:foo:2', 'Function');
+      // File index overwrites: last wins
+      expect(table.lookupExact('src/a.ts', 'foo')).toBe('func:foo:2');
+      // Global index appends
+      expect(table.lookupFuzzy('foo')).toHaveLength(2);
+    });
+  });
+
+  describe('lookupExact', () => {
+    it('finds a symbol by file path and name', () => {
+      table.add('src/index.ts', 'main', 'func:main', 'Function');
+      expect(table.lookupExact('src/index.ts', 'main')).toBe('func:main');
+    });
+
+    it('returns undefined for unknown file', () => {
+      table.add('src/index.ts', 'main', 'func:main', 'Function');
+      expect(table.lookupExact('src/other.ts', 'main')).toBeUndefined();
+    });
+
+    it('returns undefined for unknown symbol name', () => {
+      table.add('src/index.ts', 'main', 'func:main', 'Function');
+      expect(table.lookupExact('src/index.ts', 'notExist')).toBeUndefined();
+    });
+
+    it('returns undefined for empty table', () => {
+      expect(table.lookupExact('src/index.ts', 'main')).toBeUndefined();
+    });
+  });
+
+  describe('lookupFuzzy', () => {
+    it('finds all definitions of a symbol across files', () => {
+      table.add('src/a.ts', 'render', 'func:a:render', 'Function');
+      table.add('src/b.ts', 'render', 'func:b:render', 'Method');
+      const results = table.lookupFuzzy('render');
+      expect(results).toHaveLength(2);
+      expect(results[0]).toEqual({ nodeId: 'func:a:render', filePath: 'src/a.ts', type: 'Function' });
+      expect(results[1]).toEqual({ nodeId: 'func:b:render', filePath: 'src/b.ts', type: 'Method' });
+    });
+
+    it('returns empty array for unknown symbol', () => {
+      expect(table.lookupFuzzy('nonexistent')).toEqual([]);
+    });
+
+    it('returns empty array for empty table', () => {
+      expect(table.lookupFuzzy('anything')).toEqual([]);
+    });
+  });
+
+  describe('getStats', () => {
+    it('returns zero counts for empty table', () => {
+      expect(table.getStats()).toEqual({ fileCount: 0, globalSymbolCount: 0 });
+    });
+
+    it('tracks unique file count correctly', () => {
+      table.add('src/a.ts', 'foo', 'func:foo', 'Function');
+      table.add('src/a.ts', 'bar', 'func:bar', 'Function');
+      table.add('src/b.ts', 'baz', 'func:baz', 'Function');
+      expect(table.getStats().fileCount).toBe(2);
+    });
+
+    it('tracks unique global symbol names', () => {
+      table.add('src/a.ts', 'foo', 'func:a:foo', 'Function');
+      table.add('src/b.ts', 'foo', 'func:b:foo', 'Function');
+      table.add('src/a.ts', 'bar', 'func:a:bar', 'Function');
+      // 'foo' and 'bar' are 2 unique global names
+      expect(table.getStats().globalSymbolCount).toBe(2);
+    });
+  });
+
+  describe('clear', () => {
+    it('resets all state', () => {
+      table.add('src/a.ts', 'foo', 'func:foo', 'Function');
+      table.add('src/b.ts', 'bar', 'func:bar', 'Function');
+      table.clear();
+      expect(table.getStats()).toEqual({ fileCount: 0, globalSymbolCount: 0 });
+      expect(table.lookupExact('src/a.ts', 'foo')).toBeUndefined();
+      expect(table.lookupFuzzy('foo')).toEqual([]);
+    });
+
+    it('allows re-adding after clear', () => {
+      table.add('src/a.ts', 'foo', 'func:foo', 'Function');
+      table.clear();
+      table.add('src/b.ts', 'bar', 'func:bar', 'Function');
+      expect(table.getStats()).toEqual({ fileCount: 1, globalSymbolCount: 1 });
+    });
+  });
+});

gitnexus/test/unit/tools.test.ts

@@ -0,0 +1,102 @@
+/**
+ * Unit Tests: MCP Tool Definitions
+ *
+ * Tests: GITNEXUS_TOOLS from tools.ts
+ * - All 7 tools are defined
+ * - Each tool has valid name, description, inputSchema
+ * - Required fields are correct
+ * - Optional repo parameter is present on tools that need it
+ */
+import { describe, it, expect } from 'vitest';
+import { GITNEXUS_TOOLS, type ToolDefinition } from '../../src/mcp/tools.js';
+
+describe('GITNEXUS_TOOLS', () => {
+  it('exports exactly 7 tools', () => {
+    expect(GITNEXUS_TOOLS).toHaveLength(7);
+  });
+
+  it('contains all expected tool names', () => {
+    const names = GITNEXUS_TOOLS.map(t => t.name);
+    expect(names).toEqual(
+      expect.arrayContaining([
+        'list_repos', 'query', 'cypher', 'context',
+        'detect_changes', 'rename', 'impact',
+      ])
+    );
+  });
+
+  it('each tool has name, description, and inputSchema', () => {
+    for (const tool of GITNEXUS_TOOLS) {
+      expect(tool.name).toBeTruthy();
+      expect(typeof tool.name).toBe('string');
+      expect(tool.description).toBeTruthy();
+      expect(typeof tool.description).toBe('string');
+      expect(tool.inputSchema).toBeDefined();
+      expect(tool.inputSchema.type).toBe('object');
+      expect(tool.inputSchema.properties).toBeDefined();
+      expect(Array.isArray(tool.inputSchema.required)).toBe(true);
+    }
+  });
+
+  it('query tool requires "query" parameter', () => {
+    const queryTool = GITNEXUS_TOOLS.find(t => t.name === 'query')!;
+    expect(queryTool.inputSchema.required).toContain('query');
+    expect(queryTool.inputSchema.properties.query).toBeDefined();
+    expect(queryTool.inputSchema.properties.query.type).toBe('string');
+  });
+
+  it('cypher tool requires "query" parameter', () => {
+    const cypherTool = GITNEXUS_TOOLS.find(t => t.name === 'cypher')!;
+    expect(cypherTool.inputSchema.required).toContain('query');
+  });
+
+  it('context tool has no required parameters', () => {
+    const contextTool = GITNEXUS_TOOLS.find(t => t.name === 'context')!;
+    expect(contextTool.inputSchema.required).toEqual([]);
+  });
+
+  it('impact tool requires target and direction', () => {
+    const impactTool = GITNEXUS_TOOLS.find(t => t.name === 'impact')!;
+    expect(impactTool.inputSchema.required).toContain('target');
+    expect(impactTool.inputSchema.required).toContain('direction');
+  });
+
+  it('rename tool requires new_name', () => {
+    const renameTool = GITNEXUS_TOOLS.find(t => t.name === 'rename')!;
+    expect(renameTool.inputSchema.required).toContain('new_name');
+  });
+
+  it('detect_changes tool has no required parameters', () => {
+    const detectTool = GITNEXUS_TOOLS.find(t => t.name === 'detect_changes')!;
+    expect(detectTool.inputSchema.required).toEqual([]);
+  });
+
+  it('list_repos tool has no parameters', () => {
+    const listTool = GITNEXUS_TOOLS.find(t => t.name === 'list_repos')!;
+    expect(Object.keys(listTool.inputSchema.properties)).toHaveLength(0);
+    expect(listTool.inputSchema.required).toEqual([]);
+  });
+
+  it('all tools except list_repos have optional repo parameter', () => {
+    for (const tool of GITNEXUS_TOOLS) {
+      if (tool.name === 'list_repos') continue;
+      expect(tool.inputSchema.properties.repo).toBeDefined();
+      expect(tool.inputSchema.properties.repo.type).toBe('string');
+      // repo should never be required
+      expect(tool.inputSchema.required).not.toContain('repo');
+    }
+  });
+
+  it('detect_changes scope has correct enum values', () => {
+    const detectTool = GITNEXUS_TOOLS.find(t => t.name === 'detect_changes')!;
+    const scopeProp = detectTool.inputSchema.properties.scope;
+    expect(scopeProp.enum).toEqual(['unstaged', 'staged', 'all', 'compare']);
+  });
+
+  it('impact relationTypes is array of strings', () => {
+    const impactTool = GITNEXUS_TOOLS.find(t => t.name === 'impact')!;
+    const relProp = impactTool.inputSchema.properties.relationTypes;
+    expect(relProp.type).toBe('array');
+    expect(relProp.items).toEqual({ type: 'string' });
+  });
+});

gitnexus/test/unit/tree-sitter-queries.test.ts

@@ -0,0 +1,317 @@
+import { describe, it, expect } from 'vitest';
+import {
+  TYPESCRIPT_QUERIES,
+  JAVASCRIPT_QUERIES,
+  PYTHON_QUERIES,
+  JAVA_QUERIES,
+  C_QUERIES,
+  GO_QUERIES,
+  CPP_QUERIES,
+  CSHARP_QUERIES,
+  RUST_QUERIES,
+  PHP_QUERIES,
+  SWIFT_QUERIES,
+  LANGUAGE_QUERIES,
+} from '../../src/core/ingestion/tree-sitter-queries.js';
+import { SupportedLanguages } from '../../src/config/supported-languages.js';
+
+describe('tree-sitter queries', () => {
+  describe('LANGUAGE_QUERIES map', () => {
+    it('has entries for all supported languages', () => {
+      const allLanguages = Object.values(SupportedLanguages);
+      for (const lang of allLanguages) {
+        expect(LANGUAGE_QUERIES[lang]).toBeDefined();
+        expect(LANGUAGE_QUERIES[lang].length).toBeGreaterThan(0);
+      }
+    });
+
+    it('maps to the correct query constants', () => {
+      expect(LANGUAGE_QUERIES[SupportedLanguages.TypeScript]).toBe(TYPESCRIPT_QUERIES);
+      expect(LANGUAGE_QUERIES[SupportedLanguages.JavaScript]).toBe(JAVASCRIPT_QUERIES);
+      expect(LANGUAGE_QUERIES[SupportedLanguages.Python]).toBe(PYTHON_QUERIES);
+      expect(LANGUAGE_QUERIES[SupportedLanguages.Java]).toBe(JAVA_QUERIES);
+      expect(LANGUAGE_QUERIES[SupportedLanguages.C]).toBe(C_QUERIES);
+      expect(LANGUAGE_QUERIES[SupportedLanguages.Go]).toBe(GO_QUERIES);
+      expect(LANGUAGE_QUERIES[SupportedLanguages.CPlusPlus]).toBe(CPP_QUERIES);
+      expect(LANGUAGE_QUERIES[SupportedLanguages.CSharp]).toBe(CSHARP_QUERIES);
+      expect(LANGUAGE_QUERIES[SupportedLanguages.Rust]).toBe(RUST_QUERIES);
+      expect(LANGUAGE_QUERIES[SupportedLanguages.PHP]).toBe(PHP_QUERIES);
+      expect(LANGUAGE_QUERIES[SupportedLanguages.Swift]).toBe(SWIFT_QUERIES);
+    });
+  });
+
+  describe('TypeScript queries', () => {
+    it('captures class declarations', () => {
+      expect(TYPESCRIPT_QUERIES).toContain('class_declaration');
+      expect(TYPESCRIPT_QUERIES).toContain('@definition.class');
+    });
+
+    it('captures interface declarations', () => {
+      expect(TYPESCRIPT_QUERIES).toContain('interface_declaration');
+      expect(TYPESCRIPT_QUERIES).toContain('@definition.interface');
+    });
+
+    it('captures function declarations', () => {
+      expect(TYPESCRIPT_QUERIES).toContain('function_declaration');
+      expect(TYPESCRIPT_QUERIES).toContain('@definition.function');
+    });
+
+    it('captures method definitions', () => {
+      expect(TYPESCRIPT_QUERIES).toContain('method_definition');
+      expect(TYPESCRIPT_QUERIES).toContain('@definition.method');
+    });
+
+    it('captures arrow functions in variable declarations', () => {
+      expect(TYPESCRIPT_QUERIES).toContain('arrow_function');
+    });
+
+    it('captures imports', () => {
+      expect(TYPESCRIPT_QUERIES).toContain('import_statement');
+      expect(TYPESCRIPT_QUERIES).toContain('@import');
+    });
+
+    it('captures call expressions', () => {
+      expect(TYPESCRIPT_QUERIES).toContain('call_expression');
+      expect(TYPESCRIPT_QUERIES).toContain('@call');
+    });
+
+    it('captures heritage (extends/implements)', () => {
+      expect(TYPESCRIPT_QUERIES).toContain('@heritage.extends');
+      expect(TYPESCRIPT_QUERIES).toContain('@heritage.implements');
+    });
+  });
+
+  describe('JavaScript queries', () => {
+    it('captures function and class definitions', () => {
+      expect(JAVASCRIPT_QUERIES).toContain('@definition.class');
+      expect(JAVASCRIPT_QUERIES).toContain('@definition.function');
+      expect(JAVASCRIPT_QUERIES).toContain('@definition.method');
+    });
+
+    it('captures heritage (extends)', () => {
+      expect(JAVASCRIPT_QUERIES).toContain('@heritage.extends');
+    });
+
+    it('does not have interface declarations', () => {
+      expect(JAVASCRIPT_QUERIES).not.toContain('interface_declaration');
+    });
+  });
+
+  describe('Python queries', () => {
+    it('captures class and function definitions', () => {
+      expect(PYTHON_QUERIES).toContain('class_definition');
+      expect(PYTHON_QUERIES).toContain('function_definition');
+    });
+
+    it('captures imports including from-imports', () => {
+      expect(PYTHON_QUERIES).toContain('import_statement');
+      expect(PYTHON_QUERIES).toContain('import_from_statement');
+    });
+
+    it('captures heritage (class inheritance)', () => {
+      expect(PYTHON_QUERIES).toContain('@heritage.extends');
+    });
+  });
+
+  describe('Java queries', () => {
+    it('captures all major declaration types', () => {
+      expect(JAVA_QUERIES).toContain('@definition.class');
+      expect(JAVA_QUERIES).toContain('@definition.interface');
+      expect(JAVA_QUERIES).toContain('@definition.enum');
+      expect(JAVA_QUERIES).toContain('@definition.method');
+      expect(JAVA_QUERIES).toContain('@definition.constructor');
+      expect(JAVA_QUERIES).toContain('@definition.annotation');
+    });
+
+    it('captures extends and implements heritage', () => {
+      expect(JAVA_QUERIES).toContain('@heritage.extends');
+      expect(JAVA_QUERIES).toContain('@heritage.implements');
+    });
+  });
+
+  describe('C queries', () => {
+    it('captures function definitions', () => {
+      expect(C_QUERIES).toContain('function_definition');
+      expect(C_QUERIES).toContain('@definition.function');
+    });
+
+    it('captures struct, union, enum, typedef', () => {
+      expect(C_QUERIES).toContain('@definition.struct');
+      expect(C_QUERIES).toContain('@definition.union');
+      expect(C_QUERIES).toContain('@definition.enum');
+      expect(C_QUERIES).toContain('@definition.typedef');
+    });
+
+    it('captures macros', () => {
+      expect(C_QUERIES).toContain('@definition.macro');
+    });
+
+    it('captures includes as imports', () => {
+      expect(C_QUERIES).toContain('preproc_include');
+    });
+  });
+
+  describe('Go queries', () => {
+    it('captures function and method declarations', () => {
+      expect(GO_QUERIES).toContain('function_declaration');
+      expect(GO_QUERIES).toContain('method_declaration');
+    });
+
+    it('captures struct and interface types', () => {
+      expect(GO_QUERIES).toContain('@definition.struct');
+      expect(GO_QUERIES).toContain('@definition.interface');
+    });
+
+    it('captures import declarations', () => {
+      expect(GO_QUERIES).toContain('import_declaration');
+    });
+  });
+
+  describe('C++ queries', () => {
+    it('captures class, struct, namespace', () => {
+      expect(CPP_QUERIES).toContain('@definition.class');
+      expect(CPP_QUERIES).toContain('@definition.struct');
+      expect(CPP_QUERIES).toContain('@definition.namespace');
+    });
+
+    it('captures templates', () => {
+      expect(CPP_QUERIES).toContain('@definition.template');
+      expect(CPP_QUERIES).toContain('template_declaration');
+    });
+
+    it('captures heritage (base class)', () => {
+      expect(CPP_QUERIES).toContain('@heritage.extends');
+    });
+  });
+
+  describe('C# queries', () => {
+    it('captures all major types', () => {
+      expect(CSHARP_QUERIES).toContain('@definition.class');
+      expect(CSHARP_QUERIES).toContain('@definition.interface');
+      expect(CSHARP_QUERIES).toContain('@definition.struct');
+      expect(CSHARP_QUERIES).toContain('@definition.enum');
+      expect(CSHARP_QUERIES).toContain('@definition.record');
+      expect(CSHARP_QUERIES).toContain('@definition.delegate');
+    });
+
+    it('captures namespace declarations', () => {
+      expect(CSHARP_QUERIES).toContain('@definition.namespace');
+    });
+
+    it('captures constructor and property', () => {
+      expect(CSHARP_QUERIES).toContain('@definition.constructor');
+      expect(CSHARP_QUERIES).toContain('@definition.property');
+    });
+  });
+
+  describe('Rust queries', () => {
+    it('captures function items', () => {
+      expect(RUST_QUERIES).toContain('function_item');
+      expect(RUST_QUERIES).toContain('@definition.function');
+    });
+
+    it('captures struct, enum, trait, impl', () => {
+      expect(RUST_QUERIES).toContain('@definition.struct');
+      expect(RUST_QUERIES).toContain('@definition.enum');
+      expect(RUST_QUERIES).toContain('@definition.trait');
+      expect(RUST_QUERIES).toContain('@definition.impl');
+    });
+
+    it('captures module, const, static, macro', () => {
+      expect(RUST_QUERIES).toContain('@definition.module');
+      expect(RUST_QUERIES).toContain('@definition.const');
+      expect(RUST_QUERIES).toContain('@definition.static');
+      expect(RUST_QUERIES).toContain('@definition.macro');
+    });
+
+    it('captures trait implementation heritage', () => {
+      expect(RUST_QUERIES).toContain('@heritage.trait');
+      expect(RUST_QUERIES).toContain('@heritage.class');
+    });
+  });
+
+  describe('PHP queries', () => {
+    it('captures class, interface, trait, enum', () => {
+      expect(PHP_QUERIES).toContain('@definition.class');
+      expect(PHP_QUERIES).toContain('@definition.interface');
+      expect(PHP_QUERIES).toContain('@definition.trait');
+      expect(PHP_QUERIES).toContain('@definition.enum');
+    });
+
+    it('captures top-level function definitions', () => {
+      expect(PHP_QUERIES).toContain('function_definition');
+      expect(PHP_QUERIES).toContain('@definition.function');
+    });
+
+    it('captures method declarations', () => {
+      expect(PHP_QUERIES).toContain('method_declaration');
+      expect(PHP_QUERIES).toContain('@definition.method');
+    });
+
+    it('captures class properties', () => {
+      expect(PHP_QUERIES).toContain('property_declaration');
+      expect(PHP_QUERIES).toContain('@definition.property');
+    });
+
+    it('captures heritage (extends, implements, use trait)', () => {
+      expect(PHP_QUERIES).toContain('@heritage.extends');
+      expect(PHP_QUERIES).toContain('@heritage.implements');
+      expect(PHP_QUERIES).toContain('@heritage.trait');
+    });
+
+    it('captures namespace definitions', () => {
+      expect(PHP_QUERIES).toContain('namespace_definition');
+      expect(PHP_QUERIES).toContain('@definition.namespace');
+    });
+  });
+
+  describe('Swift queries', () => {
+    it('captures class, struct, enum', () => {
+      expect(SWIFT_QUERIES).toContain('@definition.class');
+      expect(SWIFT_QUERIES).toContain('@definition.struct');
+      expect(SWIFT_QUERIES).toContain('@definition.enum');
+    });
+
+    it('captures protocols as interfaces', () => {
+      expect(SWIFT_QUERIES).toContain('protocol_declaration');
+      expect(SWIFT_QUERIES).toContain('@definition.interface');
+    });
+
+    it('captures init declarations as constructors', () => {
+      expect(SWIFT_QUERIES).toContain('init_declaration');
+      expect(SWIFT_QUERIES).toContain('@definition.constructor');
+    });
+
+    it('captures function declarations', () => {
+      expect(SWIFT_QUERIES).toContain('function_declaration');
+      expect(SWIFT_QUERIES).toContain('@definition.function');
+    });
+
+    it('captures protocol method declarations', () => {
+      expect(SWIFT_QUERIES).toContain('protocol_function_declaration');
+      expect(SWIFT_QUERIES).toContain('@definition.method');
+    });
+
+    it('captures properties', () => {
+      expect(SWIFT_QUERIES).toContain('property_declaration');
+      expect(SWIFT_QUERIES).toContain('@definition.property');
+    });
+
+    it('captures heritage (inheritance)', () => {
+      expect(SWIFT_QUERIES).toContain('@heritage.extends');
+    });
+
+    it('captures type aliases', () => {
+      expect(SWIFT_QUERIES).toContain('typealias_declaration');
+      expect(SWIFT_QUERIES).toContain('@definition.type');
+    });
+
+    it('captures extensions as classes', () => {
+      expect(SWIFT_QUERIES).toContain('"extension"');
+    });
+
+    it('captures actors as classes', () => {
+      expect(SWIFT_QUERIES).toContain('"actor"');
+    });
+  });
+});

gitnexus/test/unit/utils.test.ts

@@ -0,0 +1,39 @@
+import { describe, it, expect } from 'vitest';
+import { generateId } from '../../src/lib/utils.js';
+
+describe('generateId', () => {
+  it('creates id from label and name', () => {
+    expect(generateId('Function', 'main')).toBe('Function:main');
+  });
+
+  it('handles labels with various node types', () => {
+    expect(generateId('File', 'src/index.ts')).toBe('File:src/index.ts');
+    expect(generateId('Class', 'UserService')).toBe('Class:UserService');
+    expect(generateId('Method', 'getData')).toBe('Method:getData');
+    expect(generateId('Folder', 'src')).toBe('Folder:src');
+    expect(generateId('Interface', 'IUser')).toBe('Interface:IUser');
+  });
+
+  it('handles special characters in name', () => {
+    expect(generateId('Function', 'path/to/file.ts:init')).toBe('Function:path/to/file.ts:init');
+  });
+
+  it('handles empty strings', () => {
+    expect(generateId('', '')).toBe(':');
+    expect(generateId('', 'name')).toBe(':name');
+    expect(generateId('label', '')).toBe('label:');
+  });
+
+  it('handles relationship IDs', () => {
+    expect(generateId('CONTAINS', 'Folder:src->File:src/index.ts')).toBe('CONTAINS:Folder:src->File:src/index.ts');
+  });
+
+  it('handles multi-language node types', () => {
+    expect(generateId('Struct', 'Point')).toBe('Struct:Point');
+    expect(generateId('Trait', 'Display')).toBe('Trait:Display');
+    expect(generateId('Impl', 'Display for Point')).toBe('Impl:Display for Point');
+    expect(generateId('Enum', 'Color')).toBe('Enum:Color');
+    expect(generateId('Namespace', 'std')).toBe('Namespace:std');
+    expect(generateId('Constructor', 'User')).toBe('Constructor:User');
+  });
+});

gitnexus/tsconfig.test.json

@@ -0,0 +1,10 @@
+{
+  "extends": "./tsconfig.json",
+  "compilerOptions": {
+    "rootDir": ".",
+    "noEmit": true,
+    "types": ["node", "vitest/globals"]
+  },
+  "include": ["src/**/*", "test/**/*"],
+  "exclude": ["test/fixtures/mini-repo/**", "test/fixtures/sample-code/**"]
+}

gitnexus/vitest.config.ts

@@ -0,0 +1,29 @@
+import { defineConfig } from 'vitest/config';
+
+export default defineConfig({
+  test: {
+    include: ['test/**/*.test.ts'],
+    testTimeout: 30000,
+    pool: 'forks',
+    singleFork: true,      // run all tests in a single fork to avoid KuzuDB native cleanup crashes
+    globals: true,
+    teardownTimeout: 1000,
+    dangerouslyIgnoreUnhandledErrors: true, // KuzuDB native destructor segfaults on fork exit — not a test failure
+    coverage: {
+      provider: 'v8',
+      include: ['src/**/*.ts'],
+      exclude: [
+        'src/cli/index.ts',          // CLI entry point (commander wiring)
+        'src/server/**',              // HTTP server (requires network)
+        'src/core/wiki/**',           // Wiki generation (requires LLM)
+      ],
+      // Ratchet these up as coverage improves — CI will fail if a PR drops below
+      thresholds: {
+        statements: 25,
+        branches: 22,
+        functions: 25,
+        lines: 25,
+      },
+    },
+  },
+});