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GitNexus/AGENTS.md
Gergő Magyar 9ff7337f1e
fix(mcp): rename query/cypher params so Claude Code can call them (#2186) 
* fix(mcp): advertise search_query/statement params for query/cypher tools (#2175)

Claude Code drops a tool-call argument named exactly 'query', making the
query and cypher tools unusable from it. Rename the advertised required
parameters to search_query and statement so the client transmits them.
Handler-side backward-compat for the legacy 'query' key follows in the
next commit.

* fix(mcp): accept search_query/statement with legacy query fallback (#2175)

Resolve the new advertised param names in the backend while still accepting
the legacy 'query' key, so curl/HTTP, other MCP clients, the CLI, the group
path, and the internal executeCypher() all keep working. Alias is normalized
once at the callTool chokepoint (covers group-forward + search alias); query()
and cypher() dual-read defensively. New name wins when both are supplied.
Updates the required-error message and adds dual-accept unit + integration
coverage.

* fix(cli): pass canonical search_query/statement params to query/cypher tools (#2175)

Stop the CLI from depending on the deprecated 'query' alias. No user-facing
change — the positional args are unchanged and the backend accepts both keys.

* fix(mcp): generators advertise search_query in query() examples (#2175)

Update the three doc/example generators (ai-context AGENTS/CLAUDE block,
skill-gen community skills, resources repo hint) so future analyze runs emit
query({search_query: ...}) — the param name Claude Code actually transmits.
Tests assert the new form is present and the legacy query({query: form is
absent (the #2059 generator-test pattern).

* docs(mcp): advertise search_query/statement in skill & guidance examples (#2175)

Sync the committed agent-facing docs to the renamed params so a Claude Code
agent following them emits the transmittable key: AGENTS.md/CLAUDE.md gitnexus
block, the canonical gitnexus/skills/* source and its installed/plugin/cursor
mirrors, and the README examples. Scoped rewrite of the two call prefixes only
(query({query: -> search_query, cypher({query: -> statement).

* style(mcp): prettier line-wrap for #2175 alias-resolution edits

* fix(review): uniform search_query precedence + cypher empty guard (#2175)

Code-review findings (correctness/adversarial/api-contract/maintainability
consensus):
- Group-mode query inverted the 'new name wins' rule: the callTool chokepoint
  backfilled params.query only when empty and the @group-forward read
  params.query directly, so a both-keys (or whitespace-legacy) group call let
  the legacy value win — unlike the local path. Replace the hidden param
  mutation with a self-contained 'search_query ?? query' resolve at the
  group-forward; precedence is now uniformly new-wins at every consumer site.
- cypher() now returns the same friendly required-param error as query() when
  neither statement nor query is supplied, instead of a raw DB prepare error.
- Document the legacy alias as permanent (third-party clients may send query=).
Adds group-forward alias tests (both-keys + legacy-only), empty/whitespace
search_query, the search-alias path, and the cypher empty-statement guard.

* fix(review): non-string alias safety + drop stale chokepoint comment (#2175)

Tri-review findings (correctness/adversarial/security + maintainability):
- Non-string statement/search_query/query (the MCP envelope is not
  schema-validated) hit .trim() and threw TypeError to the server boundary
  instead of a friendly required-param error. Introduce resolveAliasString()
  (new name wins; non-string -> undefined) used by query(), cypher(), and the
  group-forward, so all three return the structured error. Empirically verified
  (123 ?? '' -> 123, (123).trim() throws) — this overrides a critic refutation
  that mis-read ?? as a string coercion.
- Remove the stale query() comment claiming alias resolution happens at a
  callTool chokepoint; that mutation was removed earlier in this PR — each site
  resolves the alias itself.
- Document GroupToolPort.query's intentionally-narrower required type vs the
  wider LocalBackend impl.
Adds non-string and empty-new-key precedence tests.

* fix(mcp): alias falls back to legacy value when new key is blank (#2175)

PR #2186 review finding: resolveAliasString used `canonical ?? legacy`
(nullish), so an explicitly empty/whitespace new-name value (e.g.
{search_query:'', query:'real'}) won and was rejected — discarding a valid
legacy value, contradicting the 'new name wins when both supplied' intent.
Resolve to the first NON-BLANK string instead (new preferred when it carries
a real value, else legacy). Covers query(), cypher(), and the group-forward
(all route through the helper); non-string still resolves to a friendly error.
Flips the presence-based test and adds whitespace/cypher/group fallback cases.

* fix(mcp): drop legacy "query" mention from query/cypher schema descriptions (#2175)

PR #2186 review finding: the search_query/statement inputSchema descriptions
named the legacy "query" key — the exact arg Claude Code drops — and
description text is read by an LLM choosing arguments, weakly nudging it to
send "query". Trim the descriptions to their clean form and move the
legacy-alias note to a code comment next to the schema (preserved for
maintainers / non-CC clients). properties/required unchanged (no `query`).
2026-06-13 10:24:16 +01:00

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<!-- version: 1.7.0 -->
<!-- Last updated: 2026-04-23 -->
Last reviewed: 2026-04-23
**Project:** GitNexus · **Environment:** dev · **Maintainer:** repository maintainers (see GitHub)
## Scope
| Boundary | Rule |
|----------|------|
| **Reads** | `gitnexus/`, `gitnexus-web/`, `eval/`, plugin packages, `.github/`, `.gitnexus/`, docs. |
| **Writes** | Only paths required for the change; keep diffs minimal. Update lockfiles when deps change. |
| **Executes** | `npm`, `npx`, `node` under `gitnexus/` and `gitnexus-web/`; `uv run` for Python under `eval/`; documented CI/dev workflows. |
| **Off-limits** | Real `.env` / secrets, production credentials, unrelated repos, destructive git ops without confirmation. |
## Model Configuration
- **Primary:** Use a named model (e.g. Claude Sonnet 4.x). Avoid `Auto` or unversioned `latest` when reproducibility matters.
- **Notes:** The GitNexus CLI indexer does not call an LLM.
## Execution Sequence (complex tasks)
For multi-step work, state up front:
1. Which rules in this file and **[GUARDRAILS.md](GUARDRAILS.md)** apply (and any relevant Signs).
2. Current **Scope** boundaries.
3. Which **validation commands** you will run (`cd gitnexus && npm test`, `npx tsc --noEmit`).
On long threads, *"Remember: apply all AGENTS.md rules"* re-weights these instructions against context dilution.
## Claude Code hooks
**PreToolUse** hooks can block tools (e.g. `git_commit`) until checks pass. Adapt to this repo: `cd gitnexus && npm test` before commit.
## Context budget
Commands and gotchas live under **Repo reference** below and in **[CONTRIBUTING.md](CONTRIBUTING.md)**. If always-on rules grow, split into **`.cursor/rules/*.mdc`** (globs). **Cursor:** project-wide rules in `.cursor/index.mdc`. **Claude Code:** load `STANDARDS.md` only when needed.
## Reference docs
- **[ARCHITECTURE.md](ARCHITECTURE.md)**, **[CONTRIBUTING.md](CONTRIBUTING.md)**, **[GUARDRAILS.md](GUARDRAILS.md)**
- **Call & inheritance resolution (RFC #909 Ring 3):** See ARCHITECTURE.md § Scope-Resolution Pipeline. All languages resolve calls and inheritance through the scope-resolution pipeline (`Registry.lookup`, `preEmitInheritanceEdges`, `emitHeritageEdges`, `buildMro` → `MethodDispatchIndex`). **Shared code in `gitnexus/src/core/ingestion/` must not name languages** — plug language behavior in via `LanguageProvider` / `ScopeResolver` hooks. A language plugs in by implementing `ScopeResolver` (`scope-resolution/contract/scope-resolver.ts`) and registering it in `SCOPE_RESOLVERS`. (The legacy call-resolution DAG + `@heritage` capture path were removed in RING4-1 #942.)
- **Cursor:** `.cursor/index.mdc` (always-on); `.cursor/rules/*.mdc` (glob-scoped). Legacy `.cursorrules` deprecated.
- **GitNexus:** skills in `.claude/skills/gitnexus/`; MCP rules in `gitnexus:start` block below.
## PR Swarm Review (cross-CLI)
To run a production-readiness review of a GitNexus pull request from **any** AI CLI, follow
the canonical, CLI-neutral spec **[`pr-swarm-review/orchestration.md`](pr-swarm-review/orchestration.md)**
(seven read-only review personas under `pr-swarm-review/personas/`). It defines two
execution modes with the same output contract: **Swarm mode** (parallel subagents, e.g.
Claude Code) and **Solo mode** (one agent runs all lanes sequentially — Codex, Gemini,
Cursor, Copilot, or any agent reading this file). Per-CLI entrypoints are thin wrappers
listed in [`pr-swarm-review/README.md`](pr-swarm-review/README.md); edit review logic only
in the canonical files, never in the wrappers. The review is read-only — it never edits,
commits, or posts.
## Changelog
| Date | Version | Change |
|------|---------|--------|
| 2026-05-22 | 1.8.0 | Kotlin added to `MIGRATED_LANGUAGES` (registry-primary call resolution by default). Closes #1756 (companion-vs-instance dispatch) and #1757 (lambda scopes); refs #1746. RFC §6.4 corpus criterion waived (corpus-mode wiring is #927-scope); fixture criterion met. |
| 2026-04-23 | 1.7.0 | TypeScript added to `MIGRATED_LANGUAGES` (registry-primary call resolution by default). |
| 2026-04-20 | 1.6.0 | Added scope-resolution pipeline pointer (RFC #909 Ring 3); Python migrated to registry-primary. |
| 2026-04-19 | 1.5.0 | Cross-repo impact (#794): `impact`/`query`/`context` accept `repo: "@<group>"` + `service`. Removed `group_query`/`group_contracts`/`group_status` MCP tools; added `gitnexus://group/{name}/contracts` and `gitnexus://group/{name}/status` resources. |
| 2026-04-16 | 1.4.0 | Fixed: web UI description, pre-commit behavior, MCP tools (7->16), added gitnexus-shared, removed stale vite-plugin-wasm gotcha. |
| 2026-04-13 | 1.3.0 | Updated GitNexus index stats after DAG refactor. |
| 2026-03-24 | 1.2.0 | Fixed gitnexus:start block duplication. |
| 2026-03-23 | 1.1.0 | Updated agent instructions, references, Cursor layout. |
| 2026-03-22 | 1.0.0 | Initial structured header and changelog. |
---
<!-- gitnexus:start -->
# GitNexus — Code Intelligence
This project is indexed by GitNexus as **GitNexus** (26675 symbols, 35395 relationships, 300 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
> Index stale? Run `node .gitnexus/run.cjs analyze` from the project root — it auto-selects an available runner. No `.gitnexus/run.cjs` yet? `npx gitnexus analyze` (npm 11 crash → `npm i -g gitnexus`; #1939).
## Always Do
- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
- **MUST run `detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
- When exploring unfamiliar code, use `query({search_query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `context({name: "symbolName"})`.
## Never Do
- NEVER edit a function, class, or method without first running `impact` on it.
- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
- NEVER rename symbols with find-and-replace — use `rename` which understands the call graph.
- NEVER commit changes without running `detect_changes()` to check affected scope.
## Resources
| Resource | Use for |
|----------|---------|
| `gitnexus://repo/GitNexus/context` | Codebase overview, check index freshness |
| `gitnexus://repo/GitNexus/clusters` | All functional areas |
| `gitnexus://repo/GitNexus/processes` | All execution flows |
| `gitnexus://repo/GitNexus/process/{name}` | Step-by-step execution trace |
## CLI
| Task | Read this skill file |
|------|---------------------|
| Understand architecture / "How does X work?" | `.claude/skills/gitnexus/gitnexus-exploring/SKILL.md` |
| 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` |
| Work in the Ingestion area (239 symbols) | `.claude/skills/generated/ingestion/SKILL.md` |
| Work in the Extractors area (135 symbols) | `.claude/skills/generated/extractors/SKILL.md` |
| Work in the Components area (112 symbols) | `.claude/skills/generated/components/SKILL.md` |
| Work in the Lbug area (96 symbols) | `.claude/skills/generated/lbug/SKILL.md` |
| Work in the Group area (94 symbols) | `.claude/skills/generated/group/SKILL.md` |
| Work in the Cli area (92 symbols) | `.claude/skills/generated/cli/SKILL.md` |
| Work in the Configs area (92 symbols) | `.claude/skills/generated/configs/SKILL.md` |
| Work in the Type-extractors area (90 symbols) | `.claude/skills/generated/type-extractors/SKILL.md` |
| Work in the Hooks area (88 symbols) | `.claude/skills/generated/hooks/SKILL.md` |
| Work in the Unit area (80 symbols) | `.claude/skills/generated/unit/SKILL.md` |
| Work in the Cpp area (73 symbols) | `.claude/skills/generated/cpp/SKILL.md` |
| Work in the Scope-resolution area (72 symbols) | `.claude/skills/generated/scope-resolution/SKILL.md` |
| Work in the Server area (66 symbols) | `.claude/skills/generated/server/SKILL.md` |
| Work in the Local area (61 symbols) | `.claude/skills/generated/local/SKILL.md` |
| Work in the Wiki area (60 symbols) | `.claude/skills/generated/wiki/SKILL.md` |
| Work in the Workers area (57 symbols) | `.claude/skills/generated/workers/SKILL.md` |
| Work in the Embeddings area (56 symbols) | `.claude/skills/generated/embeddings/SKILL.md` |
| Work in the Typescript area (53 symbols) | `.claude/skills/generated/typescript/SKILL.md` |
| Work in the Storage area (51 symbols) | `.claude/skills/generated/storage/SKILL.md` |
| Work in the Php area (48 symbols) | `.claude/skills/generated/php/SKILL.md` |
<!-- gitnexus:end -->
## Repo reference
### Packages
| Package | Path | Purpose |
|---------|------|---------|
| **CLI/Core** | `gitnexus/` | TypeScript CLI, indexing pipeline, MCP server. Published to npm. |
| **Web UI** | `gitnexus-web/` | React/Vite thin client. All queries via `gitnexus serve` HTTP API. |
| **Shared** | `gitnexus-shared/` | Shared TypeScript types and constants. |
| Claude Plugin | `gitnexus-claude-plugin/` | Static config for Claude marketplace. |
| Cursor Integration | `gitnexus-cursor-integration/` | Static config for Cursor editor. |
| Eval | `eval/` | Python evaluation harness (Docker + LLM API keys). |
### Running services
```bash
cd gitnexus && npm run dev # CLI: tsx watch mode
cd gitnexus-web && npm run dev # Web UI: Vite on port 5173
npx gitnexus serve # HTTP API on port 4747 (from any indexed repo)
```
### Testing
**CLI / Core (`gitnexus/`)**
- `npm test` — full vitest suite (~2000 tests)
- `npm run test:unit` — unit tests only
- `npm run test:integration` — integration (~1850 tests). LadybugDB file-locking tests may fail in containers (known env issue).
- `npx tsc --noEmit` — typecheck
**Web UI (`gitnexus-web/`)**
- `npm test` — vitest (~200 tests)
- `npm run test:e2e` — Playwright (7 spec files; requires `gitnexus serve` + `npm run dev`)
- `npx tsc -b --noEmit` — typecheck
**Pre-commit hook** (`.husky/pre-commit`): formatting (prettier via lint-staged) + typecheck for staged packages. Tests do **not** run in pre-commit — CI only.
### Gotchas
- `npm install` in `gitnexus/` triggers `prepare` (builds via `tsc`) and `postinstall` (materializes the vendored grammars into `node_modules/`, then prefers a committed prebuild per platform-arch and only source-builds when none matches). A C/C++ toolchain (`python3`, `make`, `g++`) is needed only for that source-build fallback.
- The vendored grammars `tree-sitter-{c,dart,proto,swift,kotlin}` are handled uniformly: c is required; dart/proto/swift/kotlin are optional and skippable via `GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1`. Install warnings appear only when no prebuild matches the platform-arch and no toolchain is present, and are non-fatal — only that language's parsing is unavailable.
- ESLint configured via `eslint.config.mjs` (TS, React Hooks, unused-imports). No `npm run lint` script; use `npx eslint .`. Prettier runs via lint-staged. CI checks both in `ci-quality.yml`.
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