4af3b72487
* fix(lbug): never report a drop that could not happen, and gate FTS-indexed DML `CALL DROP_FTS_INDEX` is itself an FTS-extension function, so with the extension unloaded it fails with `Catalog exception: function DROP_FTS_INDEX is not defined`. `isBenignDropFtsIndexError` classifies that as "nothing to drop" — correct when the index does not exist, wrong when it does: the drop silently no-ops and the next write to that table dies at bind time with an engine message that never mentions FTS (#2841). The classifier stays pure (a message cannot tell you whether an index is live). Instead `dropFTSIndex` settles liveness with a catalog read on the ERROR path only and raises an FTS-named, remedy-bearing error when the index is present but undroppable. Adds `ensureFtsRowDmlSafe`, the FTS twin of `ensureEmbeddingRowDmlSafe` (#2623): catalog first, load FTS with the analyze policy only when an index actually gates DML. LadybugDB refuses that DML at BIND time — a DETACH DELETE matching zero rows fails exactly as hard as one matching thousands — and the indexes cannot be cleared in place, so a verdict is the only useful answer. Both gates now share one `SHOW_INDEXES` read via `readIndexCatalogRows`, so adding the FTS check costs no extra catalog round-trip. Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * fix(analyze): escalate instead of crashing when FTS blocks incremental DML The incremental writeback decided its write plan without ever asking whether row-level DML was legal. On a DB carrying FTS indexes with an unloadable FTS extension, `deleteNodesForFiles` then died mid-writeback: Binder exception: Trying to delete from an index on table File but its extension is not loaded. with no mention of FTS anywhere in the run — the only install-capable load happened in Phase 3, long after the writes (#2841). The incremental branch now reads the index catalog once and derives both extension verdicts before any DML. When FTS (or VECTOR) blocks in-place writes, the run falls through to the existing wipe-and-bulk-COPY escalation — the same answer #2623 gave for VECTOR, and the only one available, since the indexes cannot be dropped without the extension. Every blocked extension is named in the reason log, not just the first one checked: a DB can carry both a vector index and FTS indexes, and reporting half the cause is how this failure stayed mis-diagnosed. Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * test(analyze): cover the FTS DML gate, both-blocked escalation, and the drop guard New `incremental-index-extension-dml-gate.test.ts` drives the real `runFullAnalysis` against a real mini-repo and a real LadybugDB: - a DB carrying FTS indexes with FTS made unloadable escalates to a full DB write, names FTS in the log, ends with zero FTS indexes, and still has the newly committed content in the graph (pre-fix: Binder exception, exit 1); - FTS available keeps the surgical plan and the indexes; - a DB that never carried FTS indexes is not escalated (the catalog-first check must not tax FTS-less machines); - FTS and VECTOR both blocked produce ONE escalation naming both. `drop-fts-index-error-classification.test.ts` gains the two `dropFTSIndex` cases the #2841 guard turns on: live index + unloaded extension rejects with an FTS-named error, absent index still resolves. The existing classifier assertions are unchanged — it stays pure. The CLI e2e reproduces the reporter's exact journey (analyze with the extension, remove it, touch a file, analyze again) and asserts exit 0 plus an FTS-named reason. It skips visibly when the seeded extension cannot load on the host, so it can never report a false red about the fix. Mutation-verified: reverting the run-analyze gate fails the first scenario; reverting the dropFTSIndex guard fails the live-index case. Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * fix(lbug): make every catalog-gated path fail closed, and classify the drop remedy Review findings on #2854 (two-engine, 17 lanes). H3 — `ftsIndexExistsInCatalog` returned `false` when the catalog could not be read, i.e. "index absent", so `dropFTSIndex` swallowed the error and the caller proceeded as if the index were gone. That is the #2841 symptom the guard exists to make loud, and it contradicted the contract `readIndexCatalogRows` states two functions above. It now fails closed. §6.A — `ensureFtsRowDmlSafe` keyed on `index_type === 'FTS'`, which answers `undefined === 'FTS'` → false → *no gate* for a row whose shape cannot be read: fail-open, in the gate whose only job is preventing an unsafe write, while the VECTOR twin fails closed on the same input. Now only a positively-identified non-FTS index is waved through. Deliberately NOT the twin's `!== 'HASH'`: that is safe there only because it is scoped to the embedding table first, and this gate is table-agnostic — `!== 'HASH'` would let the HNSW index gate FTS DML. §5.A — `undefined` was overloaded: "caller passed nothing" and "caller tried and could not prove anything" shared one value, so a failed shared read silently became three reads and the two gates could decide from different snapshots. The failed snapshot is now representable (`INDEX_CATALOG_UNREADABLE`), leaving one unambiguous `??` in `resolveGateRows`. §5.B — both gates regained the unconditional null-connection precondition the refactor moved into the reader. §5.G — the throw's remedy now routes through `diagnoseExtensionLoad`, like `--repair-fts` and `ftsDegradedWarning`, so a missing runtime dependency is not told to reinstall. The message stays path-free (#2374/#2375). The dead positional row fallbacks are kept and marked `LADYBUGDB-CONTRACT`: removing them would turn a proven-inert hedge into a fail-open gate if a future engine returns unnamed tuples. Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * fix(analyze): never undo an explicit wipe, stage extension-forced rebuilds, report honestly Review findings on #2854 (two-engine, 17 lanes). H1 (P1, both engines) — `analyze --drop-embeddings` was silently reverted. The `--drop-embeddings` → `force` conversion sits inside the `embeddingCheckpoint` branch, so without a checkpoint the run stays incremental and reaches the gate; the flag then *deliberately* leaves `cachedEmbeddings` empty, which is exactly the rescue's trigger, so every row the operator asked to destroy was read back and restored, exit 0. Widening the rescue from `!embeddingRowDmlSafe` to `extensionForcedRebuild` moved that latent bug onto the dominant path, because every analyzed DB carries FTS indexes. Guarded on the flag itself — NOT on `shouldLoadCache`, which is false in the meta-under-reports case the rescue exists for and would have deleted the safeguard while fixing the wipe. The `--drop-embeddings --embeddings` variant is covered by the same guard. H2 — an extension-forced escalation wiped the LIVE index in place: `buildPath` was frozen ~440 lines earlier while the run was still classified incremental, so an interrupt or ENOSPC left no complete index, where main failed at bind time with it intact. Extension-forced rebuilds now build into a staging file and publish via the existing atomic swap; size-forced ones stay in place, since that trigger is the repo's own churn rather than a machine condition. H5 — the escalation log asserted a vector index "exists" and that the store "carries FTS indexes" in exactly the case the catalog read proved nothing, while the only truthful signal went to stderr rather than the IPC log. It now emits a distinct unreadable-catalog cause, and "this index carries" (which pointed at the vector index just named) reads "the graph store carries". §5.D — the write-set cause was dropped whenever an extension cause co-occurred; causes are appended now, not selected between. §5.C — after an FTS-forced rebuild stamped lastCommit, a plain rerun on the same commit hit the alreadyUpToDate fast path before Phase 3, so the CLI's "install … then rerun" advice could never restore FTS. The fast path is now bypassed when meta records FTS unavailable and the extension can load again, keyed on the persisted capabilities stamp rather than new state. §5.F (skip the escalation for a zero-change commit) is deliberately NOT implemented: `deleteSpringAutoConfigurationSyntheticClasses` and `deleteSpringAopEvidenceNodes` run unconditionally on the surgical branch and bind against FTS-indexed `Class`/`CodeElement`, and a zero-row DETACH DELETE fails at bind time exactly as hard as a large one — so the skip would restore the original crash. Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * perf(search): read the index catalog once per drop sweep, and state the real contract Review findings on #2854. H4 — on a machine where FTS cannot load and the DB carries no FTS index, the gate correctly returned early without loading the extension, but the surgical path still ran the full 20-entry drop sweep: every `CALL DROP_FTS_INDEX` raised "function DROP_FTS_INDEX is not defined", and the new liveness guard then fired a fresh catalog read per table — 20 reads every run, forever, for exactly the offline/load-only population, contradicting the "healthy path costs nothing" claim shipped with the guard. The sweep now reads the catalog once and skips entirely when no FTS-typed index exists. An unreadable catalog runs the sweep, so an unprovable catalog never skips real work. H8 — the docstring still promised `dropFTSIndex` "tolerates" an unloadable extension. Post-#2854 a live index plus an unloadable extension throws, and safety rests on caller ordering discipline rather than the type system — which is what would have talked the next caller out of that ordering. GUARDRAILS — the "switching to a full DB write" sign described exactly one trigger (write set >~50%). Since #2623 and #2841 an unloadable extension escalates regardless of write-set size; documented with its recovery steps. Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * test(analyze): cover the wipe guard, the staged rebuild, and the fail-closed branches Review findings on #2854. H1/H2 mutation-verified: removing `!options.dropEmbeddings` fails the new drop-embeddings case ("expected true to be false"); disabling the staging upgrade fails the staging case ("expected 0 to be greater than 0"), so both assert behaviour rather than describe it. Gate suite (7 cases): `--drop-embeddings` under an FTS-forced escalation ends at zero embedding rows and logs no "Preserving"; the escalation is one-shot — a third run on a healthy host returns to surgery and rebuilds every FTS index; an extension-forced rebuild is observed building into `lbug.staging.*` and leaves none behind; the rescue complement still preserves un-stamped rows when no wipe was requested; the never-built case now asserts the commit reached the graph. H6 — the both-blocked case hard-asserted `createVectorIndex()` while the suite probed FTS only, so it went red on any FTS-yes/VECTOR-no host. VECTOR is probed now and gates only that case, with a GITNEXUS_REQUIRE_VECTOR hard-fail. H7 — the fail-closed branches had no coverage although the VECTOR twin's test and interception technique were ready to copy: `ensureFtsRowDmlSafe` under an unreadable catalog now proves it routes to the load, and `dropFTSIndex` proves it rejects rather than silently tolerating. Plus a redaction case that forces a real path-bearing load failure — under policy `never` the assertion would have been vacuous, since that reason carries no path. §5.E/§6.B — the suite is registered in the cross-platform matrix (its sibling was; it wasn't, and GITNEXUS_REQUIRE_VECTOR is set only on that job) and moved into the sequential lbug-db project per TESTING.md:68, verified not to drop it from the sharded ubuntu job. A Windows shard weight is added as a labelled estimate — the 8s floor would skew the split it exists to protect. Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * refactor(analyze): make the FTS gate's fast path cheap, its claims provable, and its remedies classified Cleanup review of the #2841 work (four parallel angles: reuse, simplification, efficiency, altitude). Behaviour-preserving except where the previous behaviour was wrong. Correctness the review caught: - The fast-path probe keyed on `capabilities.fts.status === 'unavailable'`, which collapses "extension unavailable" and "index build failed". A deterministic build failure (an un-tokenizable row, #2544) therefore bypassed `alreadyUpToDate` on EVERY subsequent run, re-analyzed the whole repo, failed the same way, and restamped — a permanent loop where the run used to be one `stat`. Phase 3 already computes the discriminator; it is now persisted as `fts.skipReason` and the probe only runs for `extension-unavailable`. Metas written before this carry no field and keep today's behaviour. - `dropSearchFTSIndexes` skipped its sweep when no row read `index_type === 'FTS'`, while `ensureFtsRowDmlSafe` treats an unreadable type as "might be FTS". Opposite polarity, under a comment claiming they matched: a row-shape change would let the gate wave the surgical plan through while the sweep dropped nothing, putting DELETEs back on tables carrying live FTS indexes — #2589 again. The sweep now decides per configured index on identity, which is also strictly more precise. Its old justification (leftover indexes under other names) was unreachable — the loop only ever drops configured entries. - `dropFTSIndex` threw "FTS index X on table Y exists" on the one path where the catalog could not be read — a fabricated claim, on a DB the same run had just shown carries no FTS index. Presence is now `present | absent | unverifiable` and the message says which. - The remedy was hand-written for three of the four load-failure classes, discarding `missingFileRemedy`/`corruptFileRemedy`, so a corrupt extension file was told to retry an install — the misdirection #2383 fixed. Both the drop error and the escalation log now use the classified remedy. Cost, measured on a 391 MB index (cold open ~1 s, SHOW_INDEXES ~4 ms): - The probe opened the live index WRITABLE on the millisecond fast path, dragging in schema DDL, the cross-process write lock, sidecar reclaim and a CHECKPOINT on close. It is read-only now. That also closes an install trap: `doInitLbug`'s pre-load resolves the env policy on the writable branch, so an operator following our own `GITNEXUS_LBUG_EXTENSION_INSTALL=auto` advice paid a forked 15 s installer on every up-to-date run (memoized per process; the CLI is a fresh process each time). The read-only branch pins `load-only`. - A failed staged rebuild orphaned a full index-sized copy until the next lock sweep; the failure path now reclaims it. - The sweep re-read a catalog the run already held, defeating the invariant the snapshot type exists to enforce. Structure: row-shape accessors have one home, so the LADYBUGDB-CONTRACT grep claim is true by construction; staging now applies to both escalation causes, since recoverability is a property of the wipe-then-COPY plan, not of the trigger; `getExtensionCapability`/`getFtsCapability` replace hand-spelled lookups where the seam allows. Two lookups in run-analyze.ts deliberately keep the exported `getExtensionCapabilities()` form: the #2383 tests stub that export, and an ESM module mock does not intercept a helper's internal call — routing through it silently degraded the classified remedy to generic text. Recorded in-comment. Not taken, deliberately: extracting the escalation message and replacing the snapshot protocol with a connection-scoped catalog memo (both sound, both restructure code this PR just stabilised — they belong in their own change); an extension registry (premature at two instances, and the FTS/VECTOR polarity difference is exactly what it would have to parameterize back out). Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * test(analyze): pin both sides of the degraded-FTS fast-path bypass `healDegradedFts` (§5.C) had zero coverage — three separate review angles flagged it, and the cleanup pass then found it sat one conjunct away from a permanent full-re-analyze loop. Both sides are pinned now: - it re-analyzes past `alreadyUpToDate` when the stored meta says FTS is degraded and the extension loads again: run 1 analyzes with loads blocked (asserting the precondition — `status: 'unavailable'`, `skipReason: 'extension-unavailable'` — rather than assuming it), then a same-commit clean-tree rerun rebuilds every FTS index without a file changing; - it stands down when the degradation was a BUILD failure: the stored `skipReason` is rewritten to 'build-failed' and the rerun must take the fast path, because that rebuild would fail identically on every run forever. The build-failed state is reached by rewriting the stamped discriminator, not by provoking a real tokenizer failure: a genuine one needs a stored row the native tokenizer rejects (#2544/#2546), which is neither portable across the CI matrix nor deterministic, and §5.C reads only that field. Also folds the first escalation case into the one-shot case. The claim that it was fully subsumed did not hold on audit: `logs` containing 'FTS' was unique as expected, but so was the duplicate-File-node row count — every other reader goes through a Map keyed by path, which collapses a stale twin an appending rebuild would leave. Both assertions moved rather than one being dropped. Net suite runtime goes UP (two cycles removed, four added), against the cross-platform-matrix argument that motivated the dedup — recorded here because the shard weight is an estimate pending a real Windows measurement. Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * test(search): keep the whole-module adapter mock in step with the row accessors The cleanup pass moved the LadybugDB row-shape reads behind named accessors so the column contract has one home. `fts-indexes.test.ts` mocks the entire adapter module with a hand-written factory, which still exposed only the three exports the file imported before — so `verifySearchFTSIndexes` failed with "No `indexRowName` export is defined on the mock" while production was fine. The added accessors mirror the real implementations rather than returning stubs. A stub would have read `undefined` out of every catalog row and let the suite pass for the wrong reason — the failure mode a whole-module mock invites whenever the module under test grows an import. Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * revert(analyze): drop the degraded-FTS auto-heal, fix the advice it existed to justify §5.C's complaint was that the CLI tells users to "install the extension … then rerun" when a rerun lands on the up-to-date fast path and rebuilds nothing. The answer shipped for it was a probe that bypasses that fast path. Four independent problems later, the sentence is cheaper to fix than to make true: - it could not tell "extension was missing" from "index build failed" without a stamped discriminator, so a deterministic build failure (#2544/#2546) re-analyzed the entire repo on every invocation, forever, where the run used to be one `stat`; - it opened the live index on the millisecond fast path — writable at first, dragging in DDL, the cross-process lock and a CHECKPOINT (~1 s on a 391 MB index), and even read-only it is a full open; - `doInitLbug`'s pre-load resolves the env policy, so an operator following our own `GITNEXUS_LBUG_EXTENSION_INSTALL=auto` advice paid a forked 15 s installer per up-to-date run; - and it turns the fast path into a full re-analysis whenever an index authored where FTS was unavailable is later read where it loads — a legitimate, common state, and the invariant `analyzer-identity-cli.test.ts` pins. So: no probe. The degraded-search warning now points at `gitnexus analyze --repair-fts`, which rebuilds the search indexes without re-parsing the repo, instead of "then rerun". One line, no new failure modes, and it is what the issue actually asked for. `capabilities.fts.skipReason` stays in the meta stamp: it costs three lines, makes the two degradation causes distinguishable for support, and is what any future correct answer here would key on. Also gates the H2 staging assertion on the production predicate. It asserted staging unconditionally while the upgrade requires `posixSwap || windowsSwapOk`, and `windowsSwapOk` is opt-in (#2614) — so it failed on the Windows matrix for a reason unrelated to #2841. Registering this suite cross-platform is what exposed it; the assertion now mirrors the condition it is testing. Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB * fix(analyze): never stage around a damaged index — escalate in place when the catalog is unreadable CI caught this on ubuntu and macOS: `analyze-wal-checkpoint-failure` stopped failing, which is worse than it sounds. That test plants a directory at `.gitnexus/lbug.wal.checkpoint` so the auto-checkpoint's rename target is blocked, and asserts analyze exits non-zero with the `--wal-checkpoint-threshold` hint. But LadybugDB cannot open that path at all, so `CALL SHOW_INDEXES()` now fails with `IO exception: … Is a directory`. The catalog read returns UNREADABLE, both DML gates correctly fail closed, both extension loads fail with the same IO error, and the run escalates — and since the escalation stages, it built a fresh index at `lbug.staging.<uuid>`, swapped it in, and exited 0. The blocked path was never touched. The run "succeeded" while the damage sat untouched on disk, waiting to break the next in-place writeback. So the staging upgrade is now conditional on the catalog having been READ. Staging exists to protect a healthy live index from a machine-level cause (an extension that will not load); it must not be used to route around a damaged one. When we are escalating out of ignorance, build in place so the underlying IO fault lands on the failure path where the operator gets a diagnosis. Verified against the real CLI, not just the suite: with a directory planted at the checkpoint path, analyze now exits 1 and prints `gitnexus analyze --wal-checkpoint-threshold 67108864`. The healthy extension-forced case still stages (gate suite 6/6). Refs #2841 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CxokkpfssUCxvBwRZMtRCB --------- Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com> Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com> |
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GitNexus
Graph-powered code intelligence for AI agents. Index any codebase into a knowledge graph, then query it via MCP or CLI.
Works with Cursor, Claude Code, Antigravity (Google), Codex, Windsurf, Cline, OpenCode, CodeBuddy (Tencent), Qoder (Alibaba), and any MCP-compatible tool.
Why?
AI coding tools don't understand your codebase structure. They edit a function without knowing 47 other functions depend on it. GitNexus fixes this by precomputing every dependency, call chain, and relationship into a queryable graph.
Three commands to give your AI agent full codebase awareness.
Quick Start
# Index your repo (run from repo root)
npx gitnexus analyze
That's it. This indexes the codebase, installs agent skills, registers Claude Code hooks, and creates AGENTS.md / CLAUDE.md context files — all in one command.
On npm 11.x?
npxcan crash during install (Cannot destructure property 'package' of 'node.target'). Use the pnpm form instead:pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyzeSee Troubleshooting →
npx gitnexuscrashes withnode.target is null(npm 11) for the full matrix (global install, npm downgrade).
To configure MCP for your editor, run npx gitnexus setup once — or set it up manually below.
gitnexus setup auto-detects your editors and writes the correct global MCP config. You only need to run it once. To configure only selected integrations, pass --coding-agent/-c with a comma-separated list or repeat the option, for example gitnexus setup -c cursor,codex.
Editor Support
| Editor | MCP | Skills | Hooks (auto-augment) | Support |
|---|---|---|---|---|
| Claude Code | Yes | Yes | Yes (PreToolUse + PostToolUse) | Full |
| Cursor | Yes | Yes | Yes (postToolUse, manual install) | Full |
| Antigravity (Google) | Yes | Yes | Yes (AfterTool, Gemini CLI hooks schema) | Full |
| Codex | Yes | Yes | Yes (PreToolUse + PostToolUse, Codex hooks) | Full |
| OpenCode | Yes | Yes | — | MCP + Skills |
| CodeBuddy (Tencent) | Yes | Yes | — | MCP + Skills |
| Qoder (Alibaba) | Yes | Yes | — | MCP + Skills |
| Windsurf | Yes | — | — | MCP |
Claude Code and Codex get the deepest integration: MCP tools + agent skills + PreToolUse hooks that automatically enrich grep/glob/bash calls with knowledge graph context + PostToolUse hooks that detect a stale index after commits and prompt the agent to reindex.
Community Integrations
| Agent | Install | Source |
|---|---|---|
| pi | pi install npm:pi-gitnexus |
pi-gitnexus |
MCP Setup (manual)
If you prefer to configure manually instead of using gitnexus setup:
Claude Code (full support — MCP + skills + hooks)
# macOS / Linux
claude mcp add gitnexus -- npx -y gitnexus@latest mcp
# Windows
claude mcp add gitnexus -- cmd /c npx -y gitnexus@latest mcp
Codex (full support — MCP + skills + hooks)
codex mcp add gitnexus -- npx -y gitnexus@latest mcp
Codex hooks (PreToolUse graph enrichment + PostToolUse stale-index detection in ~/.codex/hooks.json, same schema as Claude Code) need the bundled adapter script, so they are installed by gitnexus setup -c codex rather than manually.
Alternatively, install everything as a Codex plugin (MCP + skills + hooks in one step):
codex plugin marketplace add abhigyanpatwari/GitNexus
# then inside Codex: /plugins → install "GitNexus"
Codex notes: SessionStart is intentionally not registered — Codex reads AGENTS.md natively, which already carries the GitNexus context block. Newly installed hooks need a one-time approval in Codex via
/hooksbefore they run. Pick one install route (gitnexus setup -c codexor the plugin): plugin hooks load alongside~/.codex/hooks.json, so installing both can fire duplicate hooks per tool call.
Cursor / Windsurf
Add to ~/.cursor/mcp.json (global — works for all projects):
{
"mcpServers": {
"gitnexus": {
"command": "npx",
"args": ["-y", "gitnexus@latest", "mcp"]
}
}
}
OpenCode
Add to ~/.config/opencode/config.json:
{
"mcp": {
"gitnexus": {
"command": "npx",
"args": ["-y", "gitnexus@latest", "mcp"]
}
}
}
CodeBuddy
CodeBuddy reads only the first existing file in its config priority chain: ~/.codebuddy/.mcp.json (recommended) → ~/.codebuddy/mcp.json (deprecated) → ~/.codebuddy.json (legacy). Edit the first non-empty file that exists — creating a higher-priority file would hide the servers in the ones below it. If none exist, create ~/.codebuddy/.mcp.json:
{
"mcpServers": {
"gitnexus": {
"command": "npx",
"args": ["-y", "gitnexus@latest", "mcp"]
}
}
}
Qoder
Add to ~/.qoder.json:
{
"mcpServers": {
"gitnexus": {
"command": "npx",
"args": ["-y", "gitnexus@latest", "mcp"]
}
}
}
How It Works
GitNexus builds a complete knowledge graph of your codebase through a multi-phase indexing pipeline:
- Structure — Walks the file tree and maps folder/file relationships
- Parsing — Extracts functions, classes, methods, and interfaces using Tree-sitter ASTs
- Resolution — Resolves imports and function calls across files with language-aware logic
- Field & Property Type Resolution — Tracks field types across classes and interfaces for deep chain resolution (e.g.,
user.address.city.getName()) - Return-Type-Aware Variable Binding — Infers variable types from function return types, enabling accurate call-result binding
- Field & Property Type Resolution — Tracks field types across classes and interfaces for deep chain resolution (e.g.,
- Clustering — Groups related symbols into functional communities
- Processes — Traces execution flows from entry points through call chains
- Search — Builds hybrid search indexes for fast retrieval
The result is a LadybugDB graph database stored locally in .gitnexus/ with full-text search and semantic embeddings.
Experimental community detection engine
Experimental — not supported for production indexes. The Icebug engine is a research path for #2337. It carries no stability guarantee, may change or be removed without a major version, and partitions differently from the default, so switching engines changes community IDs and any generated context keyed on them. Reindex with
graphologybefore relying on the output.
Community detection uses the bundled Graphology Leiden implementation by default. To try the #2337 Icebug path without changing default analyze behavior, install the optional native package alongside GitNexus and set the engine:
npm i @ladybugmem/icebug
GITNEXUS_COMMUNITY_ENGINE=icebug npx gitnexus analyze
Supported values are graphology, icebug, and auto. Today auto is behaviorally identical to icebug: both try Icebug and fall back to Graphology, while graphology skips Icebug entirely.
Icebug is not a declared dependency — its prebuilds link against system Arrow 24 (libarrow.so.2400), OpenMP, and glibc ≥ 2.38, none of which GitNexus can assume. Analyze falls back to Graphology and reports the reason in progress output when the module is missing, fails to load, or predates the setNumberOfThreads / setSeed controls that reproducible community IDs require (present at icebug-nodejs HEAD, absent from the published 12.8.0 tarball — so the fallback is what you will see today). The engine is pinned to threads: 1, randomize: false for determinism.
Note that the bundled Graphology path is no longer the slow option it once was: #2337 removed an accidental O(communities × N) copy in the vendored Leiden. On a synthetic 200k-node / 800k-edge benchmark graph it went from exceeding the 60s timeout to finishing in ~15s. Real projections vary with their degree distribution, so treat that as a direction, not a guarantee.
MCP Tools
Your AI agent gets 17 tools (15 per-repo + 2 group) automatically:
| Tool | What It Does |
|---|---|
list_repos |
Discover all indexed repositories (paginated — limit/offset) |
query |
Process-grouped hybrid search (BM25 + semantic + RRF) |
context |
360-degree symbol view — categorized refs, process participation |
impact |
Blast radius analysis with depth grouping and confidence |
trace |
Shortest directed path between two symbols (call + class-member edges) |
detect_changes |
Git-diff impact — maps changed lines to affected processes |
check |
Read-only structural checks against the indexed graph |
rename |
Multi-file coordinated rename with graph + text search |
cypher |
Raw Cypher graph queries |
route_map |
API route map — which components fetch which endpoints, and handlers |
tool_map |
MCP/RPC tool definitions — where they're defined and handled |
shape_check |
Validate API response shapes against consumers' property accesses |
api_impact |
Pre-change impact report for an API route handler |
explain |
Explain persisted taint findings (source→sink flows, --pdg indexes) |
pdg_query |
Query control/data dependence at statement level (--pdg indexes) |
group_list |
List configured repository groups |
group_sync |
Rebuild a group's Contract Registry and cross-repo links |
With one indexed repo, the
repoparam is optional. With multiple, specify which:query({search_query: "auth", repo: "my-app"}). Per-repo tools also take an optionalbranchfor indexes pinned withgitnexus analyze --branch; omitting it queries the workspace index, which follows your checked-out working tree.explainandpdg_queryneed an index built withgitnexus analyze --pdg.
MCP Resources
| Resource | Purpose |
|---|---|
gitnexus://repos |
List all indexed repositories (read first) |
gitnexus://setup |
Setup and usage guidance for agents |
gitnexus://repo/{name}/context |
Codebase stats, staleness check, and available tools |
gitnexus://repo/{name}/clusters |
All functional clusters with cohesion scores |
gitnexus://repo/{name}/cluster/{name} |
Cluster members and details |
gitnexus://repo/{name}/processes |
All execution flows |
gitnexus://repo/{name}/process/{name} |
Full process trace with steps |
gitnexus://repo/{name}/schema |
Graph schema for Cypher queries |
gitnexus://group/{name}/contracts |
A group's extracted contracts and cross-links |
gitnexus://group/{name}/status |
Staleness of repos in a group |
MCP Prompts
| Prompt | What It Does |
|---|---|
detect_impact |
Pre-commit change analysis — scope, affected processes, risk level |
generate_map |
Architecture documentation from the knowledge graph with mermaid diagrams |
CLI Commands
gitnexus setup # Configure MCP for detected editors (one-time; use -c to select)
gitnexus uninstall # Preview removal of GitNexus MCP/skills/hooks (add --force to apply)
gitnexus analyze [path] # Index a repository (or update stale index)
gitnexus analyze --repair-fts # Fast path: rebuild/verify only FTS indexes on existing index data
gitnexus analyze --force # Full rebuild: re-parse + graph rebuild + FTS rebuild
gitnexus analyze --embeddings # Enable embedding generation (slower, better search)
gitnexus embeddings install # Fetch the optional local embedding stack on demand (--cuda, --force)
gitnexus analyze --skills # Generate repo-specific skill files from detected communities
gitnexus analyze --skip-agents-md # Preserve custom AGENTS.md/CLAUDE.md gitnexus section edits
gitnexus analyze --skip-skills # Skip installing standard .claude/skills/gitnexus-* skill files
gitnexus analyze --skip-git # Index folders that are not Git repositories
gitnexus analyze --workers <n> # Parse worker pool size (>=1; default: cores-1, capped at 16)
gitnexus analyze --verbose # Log skipped files when parsers are unavailable
gitnexus analyze --max-file-size 1024 # Skip files larger than N KB (default: 512, cap: 32768)
gitnexus analyze --worker-timeout 60 # Increase worker idle timeout for slow parses
gitnexus analyze --wal-checkpoint-threshold 67108864 # 64 MiB. Control LadybugDB WAL auto-checkpoint threshold (default: 67108864 = 64 MiB; -1 keeps Ladybug stock ~16 MiB)
gitnexus mcp # Start MCP server (stdio) — serves all indexed repos
gitnexus serve # Start local HTTP server (multi-repo) for web UI
gitnexus index # Register an existing .gitnexus/ folder into the global registry
gitnexus list # List all indexed repositories
gitnexus status # Show index status for current repo
gitnexus clean # Delete index for current repo
gitnexus clean --all --force # Delete all indexes
gitnexus wiki [path] # Generate LLM-powered docs from knowledge graph
gitnexus wiki --model <model> # Wiki with custom LLM model (default: minimax/minimax-m2.5)
gitnexus wiki --base-url http://llama-box.local:8080/v1 --allow-insecure-connection llama-box.local
# Allow an exact LAN/self-hosted HTTP LLM host; env: GITNEXUS_ALLOW_INSECURE_CONNECTION
gitnexus doctor # Show runtime platform capabilities and embedding configuration
# Direct graph queries — the same tools the MCP server exposes, no MCP daemon needed
gitnexus query "<concept>" # Process-grouped hybrid search
gitnexus context <symbol> [--uid <uid> | --file <path>] # 360° symbol view; flags disambiguate a shared name
gitnexus impact <symbol> [--uid <uid> | --file <path> | --kind <kind>] # Blast radius; flags disambiguate a shared name
gitnexus trace <from> <to> # Shortest directed path between two symbols
gitnexus detect-changes # Map the working-tree diff to affected symbols and execution flows
gitnexus check # Read-only structural checks against the indexed graph
gitnexus cypher "<query>" # Run a raw Cypher query against the knowledge graph
# Repository groups (multi-repo / monorepo service tracking)
gitnexus group create <name> # Create a repository group
gitnexus group add <group> <groupPath> <registryName> # Add a repo to a group. <groupPath> is a hierarchy path (e.g. hr/hiring/backend); <registryName> is the repo's name from the registry (see `gitnexus list`)
gitnexus group remove <group> <groupPath> # Remove a repo from a group by its hierarchy path
gitnexus group list [name] # List groups, or show one group's config
gitnexus group sync <name> # Extract contracts and match across repos/services
gitnexus group contracts <name> # Inspect extracted contracts and cross-links
gitnexus group query <name> <q> # Search execution flows across all repos in a group
gitnexus group status <name> # Check staleness of repos in a group
gitnexus group impact <name> --target <symbol> --repo <groupPath> # Cross-repo blast radius
gitnexus uninstallreversesgitnexus setup— it removes the GitNexus MCP entries, hooks, and skill directories it added to each detected editor. Skill directories are identified by bundled gitnexus skill name (e.g.gitnexus-cli/), so if you customized files inside an installed skill directory, back them up first. It is a dry-run preview by default and prints the exact paths it would remove; pass--forceto apply. Per-repo indexes (gitnexus clean --all) and the global npm package (npm uninstall -g gitnexus) are left for you to remove.
Remote Embeddings
Set these env vars to use a remote OpenAI-compatible /v1/embeddings endpoint instead of the local model:
export GITNEXUS_EMBEDDING_URL=http://your-server:8080/v1
export GITNEXUS_EMBEDDING_MODEL=BAAI/bge-large-en-v1.5
export GITNEXUS_EMBEDDING_DIMS=1024 # optional, default 384
export GITNEXUS_EMBEDDING_REQUEST_DIMS=omit # optional: omit "dimensions", or an integer to override it
export GITNEXUS_EMBEDDING_API_KEY=your-key # optional, default: "unused"
export GITNEXUS_EMBEDDING_MAX_ATTEMPTS=3 # optional, total attempts (1-20)
export GITNEXUS_EMBEDDING_RETRY_CAP_MS=5000 # optional, maximum retry delay
export GITNEXUS_EMBEDDING_MIN_INTERVAL_MS=0 # optional, minimum request spacing
export GITNEXUS_EMBEDDING_HTTP_TIMEOUT_MS=180000 # optional, per-request timeout (max 300000)
gitnexus analyze . --embeddings
GITNEXUS_EMBEDDING_REQUEST_DIMS controls only the dimensions field sent in
the request body, independently of GITNEXUS_EMBEDDING_DIMS (which still
validates the returned vector's length):
omit(ornone,off,false,0) — do not senddimensionsat all, for strict backends that return the right vector size but reject the field.- a positive integer — send that value instead of
GITNEXUS_EMBEDDING_DIMS. - unset — send
GITNEXUS_EMBEDDING_DIMS(the previous behavior).
Works with Infinity, vLLM, TEI, llama.cpp, Ollama, LM Studio, or OpenAI. Retry and pacing settings are provider-neutral; provider-specific limits should be supplied through configuration. When unset, local embeddings are used unchanged.
JVM Package Sibling Injection
Java and Kotlin files in the same package receive implicit sibling class bindings
to resolve same-package references. By default, GitNexus injects at most 200
siblings per module scope, nearest first by path. Set
GITNEXUS_MAX_INJECTED_SIBLINGS=0 to remove that per-file limit; this can
substantially increase indexing work for large packages.
export GITNEXUS_MAX_INJECTED_SIBLINGS=200
gitnexus analyze .
When the limit truncates a file's sibling set, that file is marked
visibility-incomplete: same-package references still resolve through the
injected siblings, but wildcard-import attribution (used by the Spring
bean/DI/config passes) is disabled for it rather than resolved against a
partial view. Analyze logs a sibling injection truncated warning naming how
many files were affected.
Packages with more than 500 files are a separate, fixed limit: they are skipped
entirely (logged as skipping package with N files) and every file in them is
marked visibility-incomplete. GITNEXUS_MAX_INJECTED_SIBLINGS does not lift
that skip — including at 0.
Multi-Repo Support
GitNexus supports indexing multiple repositories. Each gitnexus analyze registers the repo in a global registry (~/.gitnexus/registry.json). The MCP server serves all indexed repos automatically.
Supported Languages
TypeScript, JavaScript, Python, Java, C, C++, C#, Go, Rust, PHP, Kotlin, Swift, Ruby, Dart
Language Feature Matrix
| Language | Imports | Named Bindings | Exports | Heritage | Type Annotations | Constructor Inference | Config | Frameworks | Entry Points |
|---|---|---|---|---|---|---|---|---|---|
| TypeScript | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| JavaScript | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ | ✓ | ✓ |
| Python | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Java | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
| Kotlin | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
| C# | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Go | ✓ | — | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Rust | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
| PHP | ✓ | ✓ | ✓ | — | ✓ | ✓ | ✓ | ✓ | ✓ |
| Ruby | ✓ | — | ✓ | ✓ | — | ✓ | — | ✓ | ✓ |
| Swift | — | — | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| C | — | — | ✓ | — | ✓ | ✓ | — | ✓ | ✓ |
| C++ | — | — | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
| Dart | ✓ | — | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
Imports — cross-file import resolution · Named Bindings — import { X as Y } / re-export tracking · Exports — public/exported symbol detection · Heritage — class inheritance, interfaces, mixins · Type Annotations — explicit type extraction for receiver resolution · Constructor Inference — infer receiver type from constructor calls (self/this resolution included for all languages) · Config — language toolchain config parsing (tsconfig, go.mod, etc.) · Frameworks — AST-based framework pattern detection · Entry Points — entry point scoring heuristics
Agent Skills
GitNexus ships with skill files that teach AI agents how to use the tools effectively:
- Exploring — Navigate unfamiliar code using the knowledge graph
- Debugging — Trace bugs through call chains
- Impact Analysis — Analyze blast radius before changes
- Refactoring — Plan safe refactors using dependency mapping
- Guide — GitNexus tool/resource/schema reference for the agent
- CLI — Run analyze/status/clean/wiki commands on request
- PDG Query — Statement-level control/data dependence queries (
--pdgindex) - Taint Analysis — Source→sink data-flow findings (
--pdgindex) - Plan / Work / Review / LFG — The engineering family: implementation-ready plans, gated plan execution, graph-backed change review with taint + expert lenses, and the end-to-end pipeline
Installed automatically by both gitnexus analyze (per-repo) and gitnexus setup (global). Run gitnexus analyze --skills to additionally generate each detected functional area as a direct project skill under .claude/skills/gitnexus-area-<name>/.
Requirements
- Node.js >= 22
- Git repository (uses git for commit tracking)
- Linux: glibc 2.34 or newer (Ubuntu 22.04+, RHEL/Rocky/Alma 9+, Debian 12+, Fedora 35+). The
LadybugDB native binary ships as a prebuild against that floor, so on an older host it cannot
load and reinstalling does not help — see
Linux:
GLIBC_2.34' not found. - Windows, for full-text search: the Microsoft Visual C++ 2015-2022 Redistributable (x64) and
OpenSSL 3 (
libssl-3-x64.dll,libcrypto-3-x64.dll) resolvable onPATH— see Windows: full-text search unavailable.
Release candidates
Stable releases publish to the default latest dist-tag. When a pull request
with non-documentation changes merges into main, an automated workflow also
publishes a prerelease build under the rc dist-tag, so early adopters can
try in-flight fixes without waiting for the next stable cut. (Docs-only
merges are skipped.)
# Try the latest release candidate (pre-stable — may change at any time)
npm install -g gitnexus@rc
# — or —
npx gitnexus@rc analyze
Release-candidate versions follow the standard semver prerelease format
X.Y.Z-rc.N, where X.Y.Z is the next stable target (bumped from the
current latest by patch by default; minor or major when kicking off a
bigger cycle) and N increments per published rc. Example sequence:
1.6.2-rc.1, 1.6.2-rc.2, …, then once 1.6.2 ships stable,
1.6.3-rc.1. See the Releases page
for the full list; stable latest is unaffected.
Troubleshooting
Cannot destructure property 'package' of 'node.target' as it is null
This error comes from npm 11.x's arborist while installing gitnexus (often via npx), before gitnexus code runs. It is triggered by platform-filtered optionalDependencies in native packages such as onnxruntime-node / @huggingface/transformers (used when indexing with --embeddings). GitNexus cannot catch it at runtime — use one of these workarounds:
pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyze # auto-selected when pnpm + npm 11+
npm install -g gitnexus@latest # global install avoids per-run npx reify
gitnexus analyze # if already installed globally
On pnpm 10+, lifecycle scripts are blocked unless explicitly allowed — the resolver adds --allow-build for @ladybugdb/core, gitnexus, and tree-sitter automatically when it picks pnpm dlx.
If you must stay on npm 11.x without pnpm, downgrade npm toolchain-wide (last resort):
npm install -g npm@10.9.0
See #1939 and the original #819 thread. An older variant of this crash (tree-sitter-dart tarball URL) was fixed in gitnexus v1.6.2+ (#820); if you still see install failures after upgrading, clear cache:
npm cache clean --force
npx gitnexus@latest analyze
ERR_DLOPEN_FAILED / lbugjs.node missing (pnpm dlx, pnpx)
GitNexus depends on @ladybugdb/core, whose native database addon
(lbugjs.node) is placed by a postinstall script. pnpm dlx, pnpx, and any
install run with --ignore-scripts skip lifecycle scripts, so the addon is
never put in place and the runtime crashes with ERR_DLOPEN_FAILED:
Error: dlopen(.../@ladybugdb/core/lbugjs.node, ...): tried: '...' (no such file)
code: 'ERR_DLOPEN_FAILED'
Options that run install scripts:
# pnpm dlx with explicit build permission (one-off, no global install required)
pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter \
dlx gitnexus@latest serve
# npm: global install (recommended on npm 11+; bare npx may crash — see section above)
npm install -g gitnexus@latest
gitnexus serve
# npx (npm < 11, or after upgrading npm)
npx gitnexus@latest serve
# pnpm: global install with build scripts allowed (pnpm 10.2+; no approve-builds -g on pnpm 11+)
pnpm add -g --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter gitnexus
gitnexus serve
Linux: GLIBC_2.34' not found
LadybugDB native binary (lbugjs.node) exists but failed to load:
/lib64/libc.so.6: version `GLIBC_2.34' not found (required by .../lbugjs.node)
The LadybugDB addon ships as a prebuilt binary compiled against glibc 2.34. If your distribution is older (CentOS/RHEL 8 has 2.28, Ubuntu 20.04 has 2.31, Debian 11 has 2.31), the dynamic loader cannot resolve its symbols.
Reinstalling does not help — every download delivers the same prebuilt binary. The fix is a newer C library:
- Run GitNexus on a distribution with glibc 2.34 or newer — Ubuntu 22.04+, RHEL/Rocky/Alma 9+, Debian 12+, Fedora 35+.
- Or run it in the container image, which bundles a current glibc (see Docker).
gitnexus doctor reports the required and detected glibc versions when this happens
(#2672).
Windows: full-text search unavailable
analyze completes, but keyword search is degraded and doctor shows the FTS extension failing
with Windows error 126 (The specified module could not be found). The extension needs two
runtime dependencies Windows does not ship by default:
- Microsoft Visual C++ 2015-2022 Redistributable (x64) — https://aka.ms/vs/17/release/vc_redist.x64.exe
- OpenSSL 3 —
libssl-3-x64.dllandlibcrypto-3-x64.dll, resolvable onPATH
The redistributable alone is not sufficient. If Git for Windows is installed you already have
the OpenSSL DLLs — run gitnexus from Git Bash, or prepend the directory to PATH in the
shell you use:
$env:PATH = "C:\Program Files\Git\mingw64\bin;$env:PATH"
gitnexus analyze --repair-fts
Without them the index is still built, but without search tables, so query returns empty keyword
results until you re-run gitnexus analyze --repair-fts from a shell where the DLLs resolve
(#2669).
Installation fails with native module errors
Some optional language grammars (Dart, Proto, Swift, Kotlin) require native compilation. If they fail, GitNexus still works — those languages will be skipped. To skip them intentionally (no C++ toolchain needed), set GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1 before installing.
If npm install -g gitnexus fails on native modules:
# Ensure build tools are available (Linux/macOS)
# Ubuntu/Debian: sudo apt install python3 make g++
# macOS: xcode-select --install
# Retry installation
npm install -g gitnexus
Installation fails behind an HTTP proxy (onnxruntime-node postinstall)
onnxruntime-node's postinstall downloads optional CUDA GPU binaries from api.nuget.org — outside the npm registry, so registry mirrors don't cover it, and its proxy layer (global-agent) ignores the standard HTTP_PROXY/HTTPS_PROXY variables and rejects 302 redirects (#2370).
Since the packages are optional dependencies, a failed download no longer breaks npm install -g gitnexus — npm skips the embedding stack and everything else works. The stack then self-heals on demand: the first gitnexus analyze --embeddings (or an explicit gitnexus embeddings install) fetches it through your configured npm registry — mirrors and proxies apply, no NuGet download involved — into ~/.gitnexus/embedding-runtime.
# heal a proxy-degraded install manually (CPU embeddings; registry-only)
gitnexus embeddings install
# reinstall into the prefix even when the stack already resolves
gitnexus embeddings install --force
# CUDA GPU hosts: also fetch GPU binaries (NuGet; set the proxy global-agent reads)
GLOBAL_AGENT_HTTPS_PROXY=<proxy-url> gitnexus embeddings install --cuda
The prefix defaults to ~/.gitnexus/embedding-runtime; set GITNEXUS_EMBEDDING_RUNTIME_DIR to install it elsewhere (e.g. a writable path in a container).
Node requirement for the on-demand prefix: the self-heal loads the prefixed packages via
module.registerHooks, available on Node ≥ 22.15 (on the 22.x line) or ≥ 23.5 (on the 23.x line). On an older Node the packages install but can't be loaded from the prefix — reinstall them into the install itself instead (works on every supported Node):ONNXRUNTIME_NODE_INSTALL=skip npm install -g gitnexus(Windows:set ONNXRUNTIME_NODE_INSTALL=skip && npm install -g gitnexus). Skipping only the CUDA download keeps full CPU embeddings (CPU embeddings don't need it). Check the result any time withgitnexus doctor(Embeddings → Support line).
Analyze warns about unavailable FTS or VECTOR extensions
GitNexus uses optional DuckDB extensions for BM25 and vector search. The gitnexus serve and MCP read paths only ever try to LOAD the extensions — they never block on a network install. The analyze command, by default, attempts one bounded out-of-process install if LOAD fails (a plain INSTALL to download a missing extension, escalating to FORCE INSTALL only when the LOAD error shows the existing file is broken or truncated, so a permanent non-file failure does not re-download on every run) and proceeds even when that install times out, so the index is always written to disk; BM25/vector search degrade gracefully until the extensions become available.
Configure the behavior with these environment variables:
| Variable | Values | Default | Effect |
|---|---|---|---|
GITNEXUS_LBUG_EXTENSION_INSTALL |
auto, load-only, never |
auto |
auto runs one bounded install if LOAD fails — a plain INSTALL, escalating to FORCE INSTALL only when the LOAD error shows the present extension file is broken. load-only only uses already-installed extensions (recommended for offline / firewalled environments). never skips optional extensions entirely. |
GITNEXUS_LBUG_EXTENSION_INSTALL_TIMEOUT_MS |
positive integer | 15000 |
Wall-clock budget for the out-of-process extension-install child before it is killed. |
GITNEXUS_FTS_STEMMER |
supported LadybugDB stemmer | porter |
Stemmer used when rebuilding BM25/FTS indexes. Use none for CJK-heavy repositories, or a language stemmer such as german, french, or spanish when that better matches repository comments and identifiers. Re-run gitnexus analyze --repair-fts after changing it. |
GITNEXUS_FTS_CJK_SEGMENTATION |
none, bigram |
none |
bigram inserts overlapping character-bigram boundaries into Chinese/Japanese Han-ideograph spans in content/description before FTS indexing, so LadybugDB's space-only tokenizer can see sub-phrase word boundaries. Scoped to CJK Unified Ideographs only — Japanese Hiragana/Katakana and Korean Hangul are not currently segmented. Unlike GITNEXUS_FTS_STEMMER, this rewrites stored text — enabling it on an already-indexed repo requires a full gitnexus analyze --force; neither --repair-fts nor a plain incremental analyze applies it to previously-indexed files. Set the same value wherever analyze and search-serving processes (CLI query, MCP server, web server) run. |
GITNEXUS_STREAM_GRAPH_EMIT |
0, 1 |
1 (on) |
On by default on a full rebuild (--force); incremental runs ignore it. Holds structural relationships (CALLS, IMPORTS, ACCESSES, CONTAINS, ...) as CSV-on-disk plus compact in-memory columns instead of as objects in three overlapping indexes, cutting peak in-memory graph heap by ~1.4x at no measurable CPU cost (measured A/B on a synthetic 400k-node / 1.08M-edge graph: 819 MB -> 584 MB, iteration at parity, scaling verified linear from 100k to 800k nodes, with every edge still visible through the graph interface; no end-to-end measurement on a real repository yet). Nothing is traded away — community detection, process extraction, PDG taint summaries and the local-symbol pruner all read a complete relationship set and behave identically. Set to 0 only to bisect a suspected streaming-related fault. |
GITNEXUS_COMMUNITY_ENGINE |
graphology, icebug, auto |
graphology |
Community-detection engine used during analyze. graphology is the supported default. icebug and auto are experimental and currently behave identically: both try the optional @ladybugmem/icebug native Leiden over a CSR export and fall back to Graphology if it is not installed, cannot load, or lacks the deterministic thread/seed controls. Experimental engines partition differently, so community IDs are not comparable across engines. |
GITNEXUS_WAL_CHECKPOINT_THRESHOLD |
integer >= -1 |
67108864 (64 MiB) |
LadybugDB WAL auto-checkpoint threshold during analyze (bytes). Auto-checkpoint remains enabled; -1 keeps Ladybug's stock ~16 MiB. Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments. |
GITNEXUS_LBUG_BUFFER_POOL_SIZE |
integer >= 0 (bytes) |
min(2 GiB, 80% RAM) | LadybugDB buffer-pool ceiling for every GitNexus database (analyze, MCP server, serve, group bridges). Bounded so a long-lived gitnexus mcp process or a large incremental analyze cannot grow toward LadybugDB's native 80%-of-RAM default and OOM the host (#2557). 0 restores that native unbounded default; invalid values warn and fall back to the default. During analyze the pool is right-sized to the graph and, on non-4 KiB-page hosts (Apple Silicon 16 KiB, Ascend/aarch64 64 KiB), scaled by the page-size granule ratio up to min(2 GiB × pageSize/4 KiB, 80% RAM) (#2631); this env var overrides all of that as an absolute value. |
GITNEXUS_LBUG_MAX_DB_SIZE |
positive integer (bytes) | 17179869184 (16 GiB) |
Upper bound for a single LadybugDB database file. This is an mmap/disk-address-space ceiling, not a memory limit — it does not constrain the buffer pool (use GITNEXUS_LBUG_BUFFER_POOL_SIZE for that). Raise it when indexing genuinely huge monorepos; invalid values silently fall back to the default. |
# Offline/airgapped: never reach the network for extensions
GITNEXUS_LBUG_EXTENSION_INSTALL=load-only npx gitnexus analyze
# Slow network: give extension downloads more time
GITNEXUS_LBUG_EXTENSION_INSTALL_TIMEOUT_MS=30000 npx gitnexus analyze
# CJK-heavy codebase: rebuild keyword indexes without English stemming
GITNEXUS_FTS_STEMMER=none npx gitnexus analyze --repair-fts
# CJK-heavy codebase: enable sub-phrase search over Chinese/Japanese Han text.
# On an already-indexed repo, the first run after enabling this MUST be --force —
# --repair-fts and plain incremental `analyze` both leave old files un-segmented.
GITNEXUS_FTS_CJK_SEGMENTATION=bigram npx gitnexus analyze --force
Analysis runs out of memory
Memory management is automatic: analyze sizes its heap to the machine
(always below physical RAM), caps each parse worker, and — rather than
grinding into a GC death spiral or crash — stops early with a message telling
you the one thing to do. Repeated
Replacement worker did not report ready within 5000ms warnings on a large
repository are part of the same picture: memory pressure starving healthy
workers, not a worker bug (#2649).
If analyze says the repository doesn't fit, do what the message says:
- The machine has more memory to give (a
NODE_OPTIONS--max-old-space-sizepin from your environment is holding analyze back): re-run without the pin — no flags needed. - The machine is the ceiling: shrink the scope (exclude generated or vendored directories, below) or use a machine with more RAM.
Escape hatches (GITNEXUS_MEMORY=off to decline the autopilot,
GITNEXUS_WORKER_HEAP_MB to size workers yourself) are listed in the
environment-variable table below —
most users never need them.
For very large repositories:
# Increase Node.js heap size
NODE_OPTIONS="--max-old-space-size=16384" npx gitnexus analyze
# Exclude large directories (this repo only)
echo "vendor/" >> .gitnexusignore
echo "dist/" >> .gitnexusignore
# Exclude a directory across every repo you index, without touching each
# repo's own .gitnexusignore or needing push/commit access to it. GitNexus
# reads the same sources `git` itself does: core.excludesFile (all repos)
# and $GIT_DIR/info/exclude (this repo only, untracked). A repo's own
# .gitignore/.gitnexusignore can still override either with a `!pattern`
# negation. Skip both entirely with GITNEXUS_NO_GLOBAL_IGNORE=1.
git config --global core.excludesFile ~/.gitignore_global # applies to every repo
echo "docs/" >> ~/.gitignore_global
echo "build/" >> .git/info/exclude # this repo only, untracked
Large files are being skipped
By default the walker skips files larger than 512 KB (see log line Skipped N large files (>512KB)). Raise the threshold via either the CLI flag or the environment variable — both accept a value in KB:
# CLI flag (takes precedence over the env var)
npx gitnexus analyze --max-file-size 2048 # skip only files > 2 MB
# Environment variable (persists across commands)
export GITNEXUS_MAX_FILE_SIZE=2048
npx gitnexus analyze
Values above 32768 KB (32 MB) are clamped to the tree-sitter parser ceiling; invalid values fall back to the 512 KB default with a one-time warning. When an override is active, analyze prints the effective threshold in its startup banner (e.g. GITNEXUS_MAX_FILE_SIZE: effective threshold 2048KB (default 512KB)).
Analyze reports a worker timeout
Worker parse timeouts are recoverable. GitNexus retries stalled worker jobs with backoff, splits large jobs to isolate slow files, and quarantines a file that repeatedly crashes its worker (respawning the slot so the pool keeps going). If a large repository needs more time per worker job, use either:
# CLI flag, in seconds
npx gitnexus analyze --worker-timeout 60
# Environment variable, in milliseconds
export GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS=60000
npx gitnexus analyze
For repositories with very large source files, GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES controls the worker job byte budget. The default is 8388608 bytes (8 MB).
Worker pool resilience tuning
Four env vars expose the pool's resilience layers (respawn budget, cumulative-timeout cap, circuit breaker, startup handshake). Defaults are tuned for typical repos; bump them when an analyze legitimately needs more retries, or lower them to fail-fast on a known-bad shape.
| Variable | Default | Effect |
|---|---|---|
GITNEXUS_WORKER_MAX_RESPAWNS_PER_SLOT |
3 |
Max replacement spawns per slot before the slot is dropped from the active rotation. |
GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS |
5 × subBatchTimeoutMs |
Total retry wall-time budget per job before quarantining. Bounds exponentially-growing retry waits. |
GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD |
max(3, poolSize) |
Per-slot consecutive deaths before the pool's circuit breaker trips. After tripping, dispatches require a fresh pool. |
GITNEXUS_WORKER_SHUTDOWN_DRAIN_MS |
30000 |
Max wait at pool shutdown for a retired worker still inside native code — terminated at its next JS-safe point instead of mid-native-call, which would abort the process (Napi::Error, #2432). |
GITNEXUS_WORKER_READY_TIMEOUT_MS |
5000 |
Startup budget for a parse worker to load its grammar bindings and report {type:'ready'}. Slots that miss it are treated as startup crashes. Raise it on a slow or heavily loaded host where a full pool cold-starting concurrently needs more than 5s. |
GITNEXUS_MEMORY |
off |
unset (autopilot on) |
GITNEXUS_WORKER_HEAP_MB |
clamp(512, RAM/2/poolSize, 4096) |
Per-worker V8 old-generation heap cap (#2649). Bounds pool RSS on large repos; a worker exceeding it dies with a real heap error handled by quarantine/respawn. |
GITNEXUS_SERVER_ANALYZE_HEAP_MB |
min(8192, auto cap) |
Heap for the web/MCP server's forked analyze worker (#2649). Defaults to the historical 8192 MB bounded by the machine/container's RAM-aware auto cap; set an absolute MB value to override. |
GITNEXUS_CPP_CAPTURE_BUDGET_MS |
20000 |
Per-file wall-clock budget for C++ capture extraction; on breach the file keeps partial captures with a warning (#2432). 0 expires immediately. |
Graph cleanup tuning
After scope resolution, analyze prunes inert block-local value symbols (a function-local const/let/var that ends up with only its structural File→DEFINES edge) to keep the graph focused on cross-symbol relationships. Module/file-scope symbols, class members, and any local with a real edge are always kept.
| Variable | Default | Effect |
|---|---|---|
GITNEXUS_KEEP_LOCAL_VALUE_SYMBOLS |
unset | Set to 1/true to keep inert block-local value symbols instead of pruning them. |
Programmatic callers can pass keepLocalValueSymbols: true in PipelineOptions instead of setting the env var.
Scope-resolution property-key dispatch cap
During scope resolution GitNexus synthesizes CALLS edges through property-key
dispatch — call sites like hooks.emitScopeCaptures() where a property key is
registered by multiple definitions across the codebase. To keep this fan-in
bounded, each property key is capped at 32 registrations: a key registered
by more than 32 distinct functions is skipped entirely (no CALLS are synthesized
through it), and the dropped key names are surfaced in the analyze log for
operator visibility. The cap is calibrated at 2× this repo's own provider table
(16 legitimate registrations, one per language provider).
| Variable | Default | Effect |
|---|---|---|
GITNEXUS_MAX_PROPERTY_DISPATCH_FANOUT |
32 |
Per-property-key registration cap in the property-dispatch scope-resolution pass. Set to a positive integer to raise it for repositories whose provider/hook tables exceed the default and lose CALLS coverage on a legitimate key; non-integer or < 1 values fall back to 32. Lowering it tightens the overflow budget. |
# A property key registered by 40 functions overflows the default 32 and drops
# all CALLS through it — raise the cap for that repo and rebuild so scope
# resolution reruns.
export GITNEXUS_MAX_PROPERTY_DISPATCH_FANOUT=64
npx gitnexus analyze --force
Scope-resolution dispatch-target cap
During scope resolution GitNexus resolves calls that flow through callable
values — function/method references bound to variables, passed as arguments,
or stored in maps/tables. To keep that inclusion-based resolution finite, each
callable site is capped at 32 dispatch targets. When a site gathers more
candidates than the cap it is treated as overflowed and all of its call
edges are dropped — a cliff, not a tail, so a repository with a legitimately
wide dispatch table (a single callable site resolving to 33+ targets) loses
that site's whole call chain. In that case analyze logs
callable-value-flow: candidate set exceeded the cap; no partial CALLS emitted
alongside a warning carrying the language, the overflowing context, the
candidate count, and the cap (32).
Raise the cap for such repositories:
| Variable | Default | Effect |
|---|---|---|
GITNEXUS_MAX_CALLABLE_VALUE_TARGETS |
32 |
Per-callable-site dispatch-target cap in the callable-value-flow scope-resolution pass. Set to a positive integer to raise it for repositories whose wide dispatch tables overflow the default and lose a whole call chain; non-integer or < 1 values fall back to 32. Lowering it tightens the overflow budget. |
# A callable site resolving to 48 targets overflows the default 32 and drops
# the chain — raise the cap for that repo and rebuild so scope resolution reruns.
export GITNEXUS_MAX_CALLABLE_VALUE_TARGETS=64
npx gitnexus analyze --force
Hook augmentation and skip diagnostics
The Claude Code / Antigravity hooks keep their stderr silent on normal skip
paths so strict hook runners (e.g. Codex PreToolUse) never see unexpected
diagnostic output.
When a GitNexus process holds the repo DB write lock (the common case — the MCP
server is running, or the DB-lock probe timed out and failed closed), the local
CLI augment can't run (LadybugDB is single-writer). Rather than drop the
augmentation, the hook hands the agent a short, conditional MCP-query hint on
stdout (the sanctioned additionalContext channel) — "if the GitNexus MCP tools
are live in this session, call query …" — so an agent that has the tools can
still fetch graph-ranked context. The hint is throttled to at most once per repo
per window (GITNEXUS_MCP_HINT_THROTTLE_MS, default 10 min; 0 disables), so an
owner-locked session isn't nudged on every search. A stale-index reminder, or an
already-current index, stays silent.
To see why a hook skipped the CLI augment, set GITNEXUS_DEBUG=1 and re-run the
action — the hook writes the reason (e.g. [GitNexus] augment skipped: MCP server owns DB) and the stale-index hint to its stderr:
GITNEXUS_DEBUG=1 <your command> # surfaces hook skip/diagnostic reasons on stderr
Only GITNEXUS_DEBUG=1 and GITNEXUS_DEBUG=true enable diagnostics; every other
value (including 0 and false) is treated as off. Diagnostics go to stderr
only — the hook's structured stdout (the JSON the agent consumes) is unaffected.
Privacy
- All processing happens locally on your machine
- No code is sent to any server
- Index stored in
.gitnexus/inside your repo (gitignored) - Global registry at
~/.gitnexus/stores only paths and metadata
Web UI
GitNexus also has a browser-based UI at gitnexus.vercel.app — 100% client-side, your code never leaves the browser.
Local Backend Mode: Run gitnexus serve and open the web UI locally — it auto-detects the server and shows all your indexed repos, with full AI chat support. No need to re-upload or re-index. The agent's tools (Cypher queries, search, code navigation) route through the backend HTTP API automatically.
License
Free for non-commercial use. Contact for commercial licensing.