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Gergő Magyar 0ce7880290
fix(scope-resolution): a closure binding is a call SOURCE in every language, and function-local values carry their own identity (closes #2699) (#2718)
* test(scope-resolution): audit the consumers of file-scoped node ids (#2699 part A)

#2699 item 4 — "audit consumers that assume file-scoped ids" — after #2695/#2714
gave function-local CALLABLES position-bearing ids. Tests and findings only; no
production change. That split is deliberate: `impact` reports
`resolveDefGraphId` at CRITICAL with 23 DIRECT dependents across 7 modules
(every language MRO builder, both Spring attachers, C++ member lookup,
tryEmitEdge, emitReferencesViaLookup, buildGraphTargetIndex, emitFreeCallFallback,
emitReceiverBoundCalls, preEmitInheritanceEdges, emitDetectedInterfaceImplementations,
phpEmitUnresolvedReceiverEdges, emitRubyMixinEdges, emitRustTraitImplEdges,
emitDartHeritageEdges), so changing that key chain is its own change, not a
rider on an audit.

A2 — detect_changes: CONCERN RESOLVED, now pinned. The worry was that an id
containing `@row:col` re-keys whenever a declaration MOVES, making every edit
look like symbol churn. It cannot: `local-backend.ts` maps diff hunks to
symbols by LINE-RANGE OVERLAP (`n.startLine`/`n.endLine`) and merely REPORTS
`n.id`. Node identity never participates in the match. New structural test
asserts the WHERE clause never gains `n.id =` or `n.id IN`, keeps the one
legitimate id-shaped predicate (the `BasicBlock:` prefix exclusion, #2082 U7),
and confirms the id is returned rather than matched. Structural in the same
idiom as `detect-changes-worktree.test.ts`, and labelled as not proving runtime
behaviour.

A1 — ANSWERED, and the answer is that #2699 is NOT fully closed by items 1-3.
The fail-closed guard is gated on `isOverloadableCallable`
(Function | Method | Constructor), so a function-local VALUE never reaches it.
Measured on a fixture: a top-level `const handler` and a function-local
`const handler` still produce ONE node, `Const:v.ts:handler`. That is the
residual half of the issue's original complaint. Pinned as a KNOWN LIMIT with
its reason (widening identity to values re-keys ~14,700 build-time nodes to
change ~800 persisted ones — the decision recorded in `parse-worker.ts`), and
deliberately NOT fixed here.

A3 — id-persisting consumers, classified:
  - detect_changes ................ SAFE (position-keyed; pinned by A2)
  - MCP impact/context/trace ...... SAFE (resolve by name/uid at query time)
  - bench fingerprints ............ SAFE (digest capture shape, not node ids)
  - rust-captures golden .......... SAFE (digests captures, not ids)
  - cfg pipeline-pdg snapshot ..... AT RISK by design — pins exact edge ids, so
    it trips whenever attribution changes. That is the gate working; #2714
    already exercised it.
  - wiki / group-contract links ... NOT id-keyed on locals (locals are never
    cross-file addressable, per the document-scoped contract of item 2).

Verified: tsc clean; 14/14 across the two touched files; `detect_changes`
reports 0 changed symbols (tests only).

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR

* fix(php): a closure binding is a call SOURCE, not only a TARGET (#2699 part B, S1)

A call made inside a closure binding was attributed to the ENCLOSING scope, so
the closure was a call TARGET but never a call SOURCE: impact(handler,
direction:"downstream") reported nothing even though the closure calls out.

Root cause, probe-measured rather than inferred. Instrumenting
pickCallerCallableDef (graph-bridge/ids.ts) to log every rejection reason shows
the closure's own scope EXISTS and its range DOES contain the call site, but its
ownedDefs is EMPTY, so the ":94" owned-callable filter drops it and attribution
falls through to the ":97" enclosing-scope fallback.

The reason is one missing query rule. javascript/query.ts pairs the binding name
with the closure via @declaration.function anchored on the INNER arrow node, so
anchor.range equals the @scope.function range and pass2AttachDeclarations
attaches the declaration to the CLOSURE's scope. No other language had that
rule — PHP, Rust, Kotlin, Ruby and Dart all captured named function
declarations only. That single omission is the entire empty-ownedDefs cause.

This ports the rule to PHP with the same anchor discipline (@declaration.function
on the inner anonymous_function / arrow_function, NOT on the
assignment_expression wrapper). PHP needs nothing else: it already declares
(anonymous_function) and (arrow_function) as @scope.function, so the rule alone
completes it.

Measured on a fixture: `$handler = function ($x) { return target($x); }` inside
outer() now emits

  Function:src/a.php:outer.$handler@3:2 -> Function:src/a.php:target

where it previously emitted `outer -> target`.

The pinned test in closure-binding-labels.test.ts asserted the OLD, wrong
behaviour by design ("to catch that asymmetry changing in EITHER direction"), so
it is INVERTED here rather than deleted, per its own instruction. Its block
comment is corrected to record the measured root cause, including that Kotlin
and Ruby will need BOTH this rule AND a relaxed kind gate (their lambda_literal
/ do_block is @scope.block deliberately, #1757), and that Dart has no closure
scope at all.

Verification: closure-binding-labels 50/50; PHP resolver suites 221/221
(php, php-coverage, php-response-shapes). detect_changes {staged}: 1 changed
symbol (PHP_SCOPE_QUERY), 0 affected processes, risk LOW.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR

* fix(rust): emit a node for a closure binding and make it a call SOURCE (#2699 part B, S3)

Rust was the one exception to #2687's "a closure bound to a name is a Function
node in every language": `let handler = || target(1);` produced NO graph node at
all, so the closure could be neither a call target nor a call source.

Needed BOTH query channels, which is the finding worth recording. Porting only
the scope-resolution rule (as S1 did for PHP) changed nothing measurable here,
because there was no node to attribute anything to:

  - languages/rust/query.ts — closure-binding declaration, @declaration.function
    on the INNER closure_expression so anchor.range aligns with the existing
    (closure_expression) @scope.function. This is what gives the closure's own
    scope a callable in ownedDefs, which is what stops pickCallerCallableDef
    falling through to the enclosing fn.
  - tree-sitter-queries.ts — @definition.function on the OUTER let_declaration.
    This emits the Function NODE that Rust never had.

Note the deliberate anchor asymmetry between the two channels: the graph-node
channel anchors the WRAPPER (matching the existing
(lexical_declaration (variable_declarator ... (arrow_function))) rule), while
the scope-resolution channel anchors the INNER closure (to align with
@scope.function). Getting these backwards silently produces either no node or
an unattributable one, so both sites carry a comment saying so.

Measured on a fixture — `let handler = || target(1);` inside outer():

  Function:src/a.rs:outer                CALLS  Function:src/a.rs:outer.handler@2:4
  Function:src/a.rs:outer.handler@2:4    CALLS  Function:src/a.rs:target

Previously the whole binding was absent and the call read as `outer -> target`.
The rule also covers `move` closures: the closure_expression node spans the
`move` keyword.

Verification: closure-binding-labels 50/50; rust.test.ts 192/192;
rust-coverage, rust-f70, rust-scope all pass; rust-captures-golden passes
UNCHANGED, so no golden regeneration was required. detect_changes {staged}:
2 changed symbols (RUST_SCOPE_QUERY, RUST_QUERIES), 0 affected processes,
risk LOW.

One caveat on the suite runs: this host times out `beforeAll` hooks at the
default 60s under load — rust.test.ts needed --hookTimeout=600000 to complete,
and a concurrent second vitest run starves worker startup entirely (every test
fails at ~5001ms). Both are host artifacts, not signal.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR

* fix(kotlin,ruby): a closure binding is a call SOURCE, via a Block-scope callable boundary (#2699 part B, S2)

Kotlin and Ruby anchor a closure on a Block-kind scope — Kotlin lambda_literal
and Ruby do_block/block are @scope.block DELIBERATELY (#1757 smart casts), so
they must not be re-kinded. pickCallerCallableDef gated its child-scope walk on
kind === 'Function', so a closure there could never become a call SOURCE.

Both halves are required; neither alone changes anything:

1. kotlin/query.ts and ruby/query.ts gain the closure-binding declaration rule,
   with @declaration.function on the INNER lambda_literal / block so its range
   aligns with the @scope.block range (the anchor discipline documented in
   javascript/query.ts). Without this the closure scope owns no callable def.

2. pickCallerCallableDef accepts a Block-kind child as a callable boundary when
   the scope IS that callable's body. Without this the kind gate still rejects.

The alignment test in (2) is the part worth scrutiny. Relaxing the kind gate to
accept ANY Block owning a callable would be a real regression: a nested
`fun foo()` declared inside a block is owned by that block, so a call made at
BLOCK level — outside foo — would be misattributed to foo. Comparing the def's
declaration position against the scope's start position discriminates them: for
a closure the declaration and the scope sit on the SAME node, so the positions
match; for a nested function the block starts at `{` while the def starts at the
declaration, so they do not. Existing Function-kind behaviour is untouched, so
every already-working language is unaffected by construction.

The comparison is base-safe: scope-extractor.ts builds a def id as
`def:<filePath>#<startLine>:<startCol>:<type>:<name>` from the same Range a
scope carries, so both sides share one coordinate base. This is called out in
the helper's docblock because `defStartLine` nearby documents its own output as
1-based, which invites a wrong "fix" (#2377 is exactly this class of hazard).

Ruby's call forms are restricted to lambda/proc by name: an unrestricted
(call block: (block)) would match ANY method call taking a block, so
`mapped = items.map { |i| ... }` would wrongly declare `mapped` a callable.
Verified against the parser: 3 matches (->, lambda, proc), map excluded.
Separate #eq? patterns rather than one #match? alternation, which is a known
hazard on this tree-sitter line.

Measured on fixtures:

  Kotlin  Function:src/A.kt:outer.handler@2:4  CALLS  Function:src/A.kt:target
  Ruby    Function:src/a.rb:outer.handler@4:2  CALLS  Method:src/a.rb:target#1

previously `outer -> target` and `outer#0 -> target#1`.

The pinned Kotlin test asserted the old behaviour by design and is INVERTED, not
deleted. Ruby had NO pinned case, so a new one is added rather than inverted.
The describe title no longer claimed something false ("not yet a call SOURCE"
now holds only for Dart) and was retitled.

Verification: closure-binding-labels 51/51; kotlin.test.ts, kotlin-coverage,
ruby.test.ts, ruby-scope, ruby-namespaced all pass (478 passed / 1 expected
inversion before the test was flipped). impact on pickCallerCallableDef:
CRITICAL, 191 impacted, ONE d=1 (resolveCallerGraphId) — the return contract is
unchanged, so that dependent is unaffected. detect_changes {staged}: 5 changed
symbols, 2 affected processes (both EmitReferencesViaLookup, one of them the new
ScopeIsCallableBody step), risk medium.

Dart remains the last failing language: dart/query.ts declares no
@scope.function at all, and dart/captures.ts synthesizes one only from a
declaration WITH a body node, which an expression-bodied closure lacks.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR

* fix(dart): give a closure binding a scope and a distinct identity (#2699 part B, S4)

Dart was the last language where a closure binding could not be a call SOURCE,
and fixing only that would have made the graph WORSE, not better. This lands
both halves together for that reason.

## The attribution half

A Dart closure had no scope at all. `dart/query.ts` declares no
@scope.function anywhere — Dart's function scopes are SYNTHESIZED in
`dart/captures.ts` from `declNode` + `findFunctionBody(declNode)`, and
`findFunctionBody` looked only at the next named SIBLING for a `function_body`.
A closure literal carries its body as a CHILD (`function_expression_body`), so
it matched nothing and no scope was produced.

`query.ts` gains the closure-binding declaration rule and `findFunctionBody`
understands the child form. Deliberately NO @scope.function is added to the
query: it would collide at identical range with the synthesized one, and
duplicate scope ids make `buildScopeTree` throw, which DROPS THE WHOLE FILE.

## The identity half, and why it is not optional

With attribution alone, two same-named closures in one file both keyed to the
bare `Function:a.dart:handler`. One node then appeared to call BOTH targets —
a CALLS edge present nowhere in the source. That is worse than the missing edge
it replaced, so S4 could not ship without this.

Root cause is not Dart-specific. `enclosingCallablePrefix` derives a SEMANTIC
relation — what encloses this callable — by SYNTACTIC ancestor walk. Dart parses
`int outer() { … }` as `function_signature` followed by `function_body` as
SIBLINGS, so the enclosing callable is never an ancestor of code inside it and
no membership set can fix that; the walk looks in the wrong direction.

This is what SCIP and real compilers avoid by construction. SCIP keeps a local
symbol opaque (`local <id>` — no name, no position, no chain) and models
containment as a SEPARATE `enclosing_symbol` field; its spec says the local/global
choice should follow ACCESSIBILITY, not the ability to name an enclosure. Dart's
own analyzer answers this from `Element.enclosingElement` in the element model,
never from AST ancestry. clang uses `name@offset` for a function-local; Kythe
uses a document-scoped VName plus a `childof` edge. Identity is positional and
opaque; enclosure is a relation.

`findSplitBodyCallableAncestor` is the narrow fix at that seam: a fallback used
ONLY when the ancestor walk finds nothing, recovering the callable from the
body's preceding sibling.

The sibling must be a BARE SIGNATURE, and that restriction is load-bearing —
"any preceding callable sibling" is WRONG and was caught regressing PHP during
this work. In `<?php function target($x) {…} $handler = function ($x) {…};` the
closure is at FILE level, so the ancestor walk correctly finds nothing, the
fallback runs, and an unrestricted version mis-qualified the file-level
`$handler` as `target.$handler`. A preceding sibling is only an ENCLOSING
callable when it cannot hold its own body.

`SPLIT_SIGNATURE_NODE_TYPES` is exactly that set and is DERIVED, not listed:
`LOCAL_SCOPE_BODY_NODE_TYPES` is already `FUNCTION_NODE_TYPES` minus the bare
signature types, so the difference between them IS the split-signature set
(`function_signature`, `method_signature` — verified at runtime). PHP's
`function_definition` carries a body and is in both, so it is excluded. No
language is named in shared code, and any future split-grammar language is
covered for free.

## Verification

Full resolver sweep — the gate that caught #2714's Rust regression — 2926
passed / 1 skipped / 0 failed across 51 files. closure-binding-labels 52/52;
dart.test.ts, dart-coverage, callable-id-lockstep, function-local-identity,
caller-identity-regression all pass (156/156 across 6 files).
impact on `enclosingCallablePrefix`: LOW, 5 impacted, 3 d=1 all inside
parse-worker. detect_changes {staged}: 5 changed symbols, 0 affected processes,
risk LOW.

Three existing Dart expectations FLIPPED rather than being deleted: Dart locals
now carry the same enclosing-callable + position identity every other language
got in #2695, so `local.dart:handler` became `local.dart:caller.handler@1:2`.
A new test pins the actual defect — two same-named closures staying DISTINCT
nodes — because the qualification assertions alone would not fail if the
fabricated edge returned.

One note for future work: an id-shape assertion here carries a call-site suffix
on indirect invocations (`…handler@3:2:5:9`) but not on direct calls. That is
the callable-value-flow pass keying its edge by invocation position, not part of
the node id.

Part B is now complete: PHP (S1), Rust (S3), Kotlin + Ruby (S2), Dart (S4).

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR

* fix(scope-resolution): close every deferred item on #2699 (A1 values, twin-list guard, schema bumps)

Clears the limitations this PR had been carrying rather than leaving them as
follow-ups.

## A1 — function-local VALUES now carry their own identity

This was #2699's ORIGINAL complaint and the one a callable-only gate could never
reach: a top-level `const handler` and a function-local `const handler`
collapsed onto ONE `Const:v.ts:handler`. #2695 restricted position-qualified
identity to Function|Method|Constructor because the collision that produced
wrong CALLS edges was between callables, and widening churned ids for symbols
the pruner mostly deletes. The churn is real and is accepted here deliberately.

Widening needed THREE gates aligned, not one:
  - id-building     — `parse-worker.ts` nestedCallablePrefix
  - resolution      — `ids.ts` position key
  - registration    — `node-lookup.ts` position-key registration

Missing the third would register no position key for values, so every lookup
misses and falls through silently. That is the #2714 failure mode: the caller
attaches to a node that does not exist and the edge is DROPPED, which looks like
"zero dangling edges" from outside. All three now route through ONE predicate,
`isPositionQualifiedLocalLabel`, rather than repeating the label set a third
time.

Only LOCALS move. The prefix comes from `enclosingCallablePrefix`, which returns
undefined when nothing encloses the declaration, so top-level and class-member
ids are untouched — verified by the full resolver sweep, where a leak onto class
members would have broken assertions in every language. `Property` is included
on purpose: a class field stays unqualified because the prefix walk boundaries
on class-likes, while an object-literal property inside a function is genuinely
local and would otherwise keep the old collision.

Measured: `Const:v.ts:handler` + `Const:v.ts:run.handler@3:2`, two distinct
nodes. The KNOWN LIMIT test is FLIPPED per its own former instruction ("this
test should be updated as part of it rather than deleted").

## Schema bumps — required by Part B, not just by A1

INCREMENTAL_SCHEMA_VERSION 20 -> 21, parse-cache SCHEMA_BUMP 27 -> 29.

SCHEMA_BUMP is 29, not 28, and that is the point of re-checking it against
origin/main at MERGE time rather than branch time. This branch cut at 27 and
bumped to 28; #2415 also bumped 27 -> 28 and merged first. The automated
main-merge onto this branch surfaced the collision — leaving it at 28 would have
shipped this whole change with NO parse-cache invalidation, so every warm cache
keeps replaying the pre-fix captures and ids. This is the third instance of that
collision recorded in parse-cache.ts (#2632/#2653 hit it at v21, and
#2653/#2654 hit INCREMENTAL_SCHEMA_VERSION the same way).

Part B already changed emitted node ids AND edges on files that did not
themselves change (Dart locals re-keyed, Rust gained a node it never emitted,
five languages gained closure-source attribution). A v20 index topped up
incrementally keeps serving the old attribution, and a warm parse cache replays
the old captures and ids verbatim. Shipping S1-S4 without these would have let
every existing index silently keep the pre-fix graph.

## Twin-list drift guard — the sixth instance in this family

`IMPLICIT_RECEIVERS` (gitnexus-shared lookup-core.ts) and `THIS_RECEIVERS`
(type-env.ts) spell the same concept in two packages, and nothing enforced
agreement — `$this` was added to the shared list in #2714 only because it was
already in the other. New structural test asserts set equality plus the ONE
deliberate asymmetry (`Me`, Visual Basic spelling, absent from the shared list
because no SupportedLanguages entry uses it) in BOTH directions, so re-adding it
there or dropping it here each fail loudly.

Structural rather than value-imported: both constants are module-private, and
exporting them purely to be testable would widen two public surfaces to satisfy
a test.

## Two false comments corrected

  - `lookup-core.ts` said "see the drift guard noted in #2714", implying a guard
    existed when it was only a deferred follow-up. It exists now, and the
    comment points at it.
  - `callable-id-lockstep.test.ts` claimed its regex "fails if any site
    reconstructs the id". It matches ONE template spelling; a hand-rolled
    concatenation still slips past. Now stated as a tripwire for the known
    shape, not a proof.

## Skill learnings

Four entries appended to eval/workflow_bench/learnings.jsonl from this run: the
v9fs safe-writer failure, backticks silently terminating a query template
literal (hit three times), a module-level TDZ const that passes tsc and then
presents as N file failures with ZERO failing assertions, and concurrent vitest
runs starving worker startup so a whole suite fails at ~5001ms.

## Verification

Full resolver sweep 2926 passed / 1 skipped / 0 failed (51 files) — identical to
pre-A1, which is the evidence that only locals moved. All EIGHT bench gates PASS
with fingerprints UNCHANGED, so no regeneration was needed. function-local-identity,
callable-id-lockstep, receiver-twin-list-drift and closure-binding-labels 71/71.
tsc --noEmit clean.

detect_changes {staged}: 9 changed symbols, 14 affected processes, risk HIGH —
expected, and the reason the sweep above is the gate rather than a targeted list.
Every affected process routes through `resolveDefGraphId`, the key chain Part A
measured at CRITICAL with 23 direct dependents.

Deliberately NOT done: the SCIP end state (opaque `local <id>` plus an explicit
enclosure EDGE instead of containment encoded in the id string). It is a design
direction, not a limitation of this work, and it is INCOMPATIBLE with A1 — A1
widens chain-encoded identity, that removes chain encoding entirely. Bundling
both would re-key every local twice. Written up in the research notes.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR

* test: update two assertions the #2699 changes correctly invalidated

Both failed on CI at da3d8397 and are fixed here. Neither is a behaviour
regression; both pinned values that this PR deliberately changed.

1. this-boundary.test.ts — "a Kotlin lambda still sees the receiver"

The `this.m()` edge still exists and `this` still resolves to the enclosing
receiver, which is the ONLY property this test exists to guard (its own comment
said so: "what matters here is only that the `this.m()` edge still exists at
all"). Only the SOURCE moved, from `run` to the lambda:

  Method:K.kt:K.run#0       -> Method:K.kt:K.run.f@2:16
  Method:K.kt:K.run.f@2:16  -> Method:K.kt:K.m#0

The comment justifying the old expectation is now false and is corrected rather
than left: it said the lambda "is not its own caller anchor" because Kotlin
scopes `lambda_literal` as a BLOCK. Kotlin still scopes it as a block (#1757 is
unchanged) — what changed in S2 is that a Block-kind scope is accepted as a
caller anchor when the scope IS the callable's body.

2. call-summary-schema-version.test.ts — INCREMENTAL_SCHEMA_VERSION pin

Moves 20 -> 21 with the bump, which is the point of pinning it: a change that
alters emitted ids or edges without bumping would otherwise ship silently.

Also adds the missing reuse-gate case. `passesReuseGate(20)` now asserts FALSE —
a v20 index predates closure bindings becoming call SOURCES, the Rust node for
`let f = || …`, the Dart closure scope + enclosing-callable identity, and
position-qualified function-local values. Topping such an index up incrementally
keeps serving the old attribution, including the Dart case where two same-named
closures collapsed onto one node and asserted a CALLS edge present nowhere in
the source.

Why CI found these and local verification did not: the verification set was
`test/integration/resolvers/` plus a hand-picked list, and both failures sat
outside it — one integration test about `this` (which a caller-attribution
change obviously touches) and one unit test pinning the exact constant that was
bumped. Grepping for the changed constant, and for tests asserting closure
attribution, would have found both. All 8 suites that reference the schema
constants were then run: 177/177, no third pin.

Verification: this-boundary + call-summary-schema-version 17/17;
the 8 schema-referencing suites 177/177. detect_changes {staged}: 0 changed
symbols, 0 affected processes, risk LOW (assertion-only edits).

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR

* fix(scope-resolution): resolve every finding from the multi-engine review of #2699 part B

The first cut of Part B shipped four P1 defects. A two-engine review (Claude
swarm + ce personas; Codex gpt-5.6-sol swarm + ce + adversarial) found all four,
three of them because an independent engine disagreed with the authoring one.
Each is fixed here and pinned in test/integration/closure-review-findings.test.ts.

## P1-1 — a multi-line closure binding fabricated a CALLS edge

The worst of the four, because it reintroduced the exact defect class #2699
exists to remove. The two query channels anchor on DIFFERENT nodes by design
(graph-node on the outer wrapper, scope-resolution on the inner closure) and the
bridge joins them on line only. Same line, the join matches. Split across lines:

    $multi =
        function ($x) { return target($x); };

the join missed, `resolveDefGraphId` failed closed, and `resolveCallerGraphId`
then CLIMBED to the parent scope — emitting `outer -> target` although `outer`
calls nothing, while the real `outer.$multi` node sat with zero outgoing edges.

`resolveCallerGraphId` now fails closed at the owning callable instead of
climbing. If we have identified the callable that owns a call site and cannot
name its graph node, crediting an ancestor is not graceful degradation — it
invents a relationship. A missing edge is the correct failure direction for a
graph whose consumers include `impact`.

Getting there took two attempts, worth recording: the first guard keyed on the
def's qualifiedName carrying the `@line:col` local marker, but that suffix is
added by parse-worker for GRAPH NODE ids and scope-resolution defs do not have
it, so the guard never fired. `pickCallerCallableDef` now reports whether the
callable came from a child scope, and the fail-closed applies to the owning
callable either way.

## P1-2 — TS constructor parameter properties were re-keyed as locals

A REGRESSION against the base, not merely an incomplete fix. Admitting
`Property` to the position-qualified set made the enclosing-callable walk reach
the constructor's `method_definition` THROUGH the parameter list — a
LOCAL_SCOPE_BODY hit that lands before any class boundary — so
`constructor(private readonly port: Port)` produced
`Property:svc.ts:Service.constructor.port@2:14` instead of `Service.port`. That
silently empties the slot `impact`, `rename` and FTS address while the class
still asserts HAS_PROPERTY against it, and it is the Angular/NestJS DI idiom.
A real instance exists in this repo at src/core/group/service.ts:304.

parse-worker.ts already computed the correct exemption (`isFunctionLocalProperty`,
lines 2245-2257) two lines above; the new ternary discarded it. Now reused, so
the owner-edge decision and the id decision cannot disagree.

## P1-3 — Dart top-level and `final` closures were never call sources

The rule matched only `initialized_variable_definition`, Dart's FUNCTION-LOCAL
shape. A top-level `var` is `initialized_identifier` and a top-level
`final`/`const` is `static_final_declaration`; the second declarator of
`var f = ..., g = ...` is also `initialized_identifier`. None got a declaration
capture, so `findFunctionBody` never synthesized their scope.
dart/captures.ts ALREADY listed all three in bindingNodeTypes for callable-flow
— the declaration rule simply did not mirror it. It does now.

## P1-4 — Ruby `do ... end` and `Proc.new` closures were uncovered

`do ... end` is the dominant MULTI-LINE Ruby style and produces `(do_block)`;
all three patterns matched `(block)` only. The scope channel already covered
both, so these closures got a Block scope owning nothing and their calls fell
through to the enclosing method. The PR's own Ruby test used the brace form, so
it passed.

Fixing it needed BOTH channels — tree-sitter-queries.ts had no graph-node rule
for the `(call)` forms either, exactly as Rust did. Verified: brace, do/end and
Proc.new are now all sources.

## Also from the review

- The split-signature fallback could fire on VALID TypeScript: a
  `declare namespace` containing a bodyless overload made the next declaration's
  `export_statement` a sibling of a `function_signature`, so `send` became
  `internalHelper.send@2:9`. The fallback now requires the matched node to be
  the signature's BODY (a body holds statements; a declaration wrapper holds
  another signature), which separates the two without naming a grammar.
- `isCallableDef` re-spelled `Function | Method | Constructor` in the same file
  that imports `isOverloadableCallable` and calls it three times — a NEW twin
  list, in the PR whose headline is a twin-list drift guard. It now delegates.
- A partial edit had left a self-contradictory comment in parse-worker.ts
  ("Restricted to CALLABLE labels: the / Applies to VALUES as well as callables").
- eval/workflow_bench/learnings.jsonl carried a "skill": "gitnexus-plan" entry,
  but that skill's SKILL.md:347 states feedback is chat-only and forbids
  appending learnings during a planning task. Dropped; the three gitnexus-work
  entries are sanctioned and stay.
- Ruby's lambda/proc patterns tested the method NAME only, so `MyMod.lambda { }`
  was captured as a closure binding. `!receiver` now constrains them.
- Rust's closure work (S3) had ZERO test coverage anywhere — verified once by a
  throwaway fixture and never pinned. Now covered.

## Verification

Full resolver sweep plus the identity/closure suites: 3017 passed / 1 skipped /
0 failed across 58 files (up from 2997 — the new tests). This is the gate that
mattered for P1-1: failing closed instead of climbing could have silently
deleted real edges in any language, and ~2900 resolver assertions say it did
not. All EIGHT bench fingerprint gates PASS with fingerprints UNCHANGED.
tsc --noEmit clean.

detect_changes {staged}: 14 changed symbols, 18 affected processes, risk
CRITICAL — expected, since P1-1 changes the fallthrough of `resolveCallerGraphId`,
the key chain Part A measured at CRITICAL with 23 direct dependents.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0184RmD24KFJidYqpM7v3XjR

---------

Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com>
Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-07-28 18:25:19 +01:00
.agents/plugins feat: full Codex support — hooks, plugin marketplace, and setup (#2328, supersedes #1131) (#2369) 2026-07-04 13:32:17 +01:00
.claude fix(ci): stop the review agent rejecting its own graph-backed reviews (#2731) 2026-07-28 17:13:29 +01:00
.claude-plugin chore: release v1.6.9 (#2367) 2026-07-04 07:53:06 +01:00
.cursor fix(storage): rename index metadata to gitnexus.json with dual-write compatibility (#2363) 2026-07-03 19:32:59 +01:00
.devcontainer fix: large-repo analyze OOM and false worker-timeout cascade (#2649) (#2679) 2026-07-25 09:16:17 +01:00
.gemini/commands feat(review): add PR reviewer swarm agents (#1851) 2026-05-29 18:24:16 +01:00
.github fix(ci): stop the review agent rejecting its own graph-backed reviews (#2731) 2026-07-28 17:13:29 +01:00
.history/gitnexus fix(test): add --repo to CLI e2e tool tests for multi-repo environment 2026-03-18 08:12:25 +00:00
.husky feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
.sisyphus/drafts fixed constructor to method relation not getting stored in kuzu issue 2026-01-26 22:58:15 +05:30
deploy/kubernetes ci(docker): mirror signed images to Docker Hub alongside GHCR (#1029) 2026-04-23 18:59:26 +01:00
Documentation Add Kilo Code + GitNexus MCP setup guide (#2259) 2026-07-02 11:04:22 +01:00
eslint-rules fix(windows): 32767-char tree-sitter crash + VECTOR extension SIGSEGV (#1433) 2026-05-10 16:00:36 +01:00
eval fix(scope-resolution): a closure binding is a call SOURCE in every language, and function-local values carry their own identity (closes #2699) (#2718) 2026-07-28 18:25:19 +01:00
gitnexus fix(scope-resolution): a closure binding is a call SOURCE in every language, and function-local values carry their own identity (closes #2699) (#2718) 2026-07-28 18:25:19 +01:00
gitnexus-claude-plugin fix(ci): stop the review agent rejecting its own graph-backed reviews (#2731) 2026-07-28 17:13:29 +01:00
gitnexus-cursor-integration fix(ci): stop the review agent rejecting its own graph-backed reviews (#2731) 2026-07-28 17:13:29 +01:00
gitnexus-shared fix(scope-resolution): a closure binding is a call SOURCE in every language, and function-local values carry their own identity (closes #2699) (#2718) 2026-07-28 18:25:19 +01:00
gitnexus-test-setup feat: merge gitnexus-mcp into gitnexus package - unified CLI+MCP 2026-02-04 01:12:41 +05:30
gitnexus-web Merge pull request #2643 from abhigyanpatwari/dependabot/npm_and_yarn/gitnexus-web/lru-cache-11.5.2 2026-07-23 11:56:12 +05:30
pr-swarm-review feat(skills): GitNexus Engineering Tool Kits (#2566) 2026-07-19 15:07:24 +01:00
.cursorrules docs: agent development framework, GitHub templates, eval refactor (#479) 2026-03-25 06:48:41 +00:00
.dockerignore fix(ci): Change docker base image from alpine to debian (#1014) 2026-04-21 21:31:58 +01:00
.env.example feat(analyze): private GitHub repos via PAT + Azure DevOps Server support (#2076, #2210) (#2223) 2026-06-16 05:49:02 +01:00
.git-blame-ignore-revs feat: configure eslint with unused import removal (#564) 2026-03-28 15:28:09 +00:00
.gitattributes feat(devcontainer): add devcontainer for Claude/Codex/Cursor CLIs (#1875) 2026-06-02 05:09:01 +01:00
.gitignore chore: stop tracking docs/plans (planning output stays local) 2026-07-21 10:09:35 +00:00
.gitleaks.toml feat(analyze): private GitHub repos via PAT + Azure DevOps Server support (#2076, #2210) (#2223) 2026-06-16 05:49:02 +01:00
.gitleaksignore chore(security): suppress deleted auth placeholder 2026-07-16 10:08:59 +07:00
.mcp.json fix: use cross-platform npx command in .mcp.json 2026-02-22 17:46:04 +00:00
.prettierignore chore(quality): exclude test/fixtures from CodeQL, ESLint, and Prettier (#1313) 2026-05-04 09:35:34 +01:00
.prettierrc feat: configure prettier with pre-commit hook (#563) 2026-03-28 14:58:04 +00:00
.windsurfrules resources implemented and agents.md and skills updated to use it 2026-02-05 05:13:48 +05:30
AGENTS.md feat(ci): review agent runs as a coordinated reviewer swarm (#2572) 2026-07-20 07:31:40 +01:00
ARCHITECTURE.md fix(scope-resolution): resolve callable reference flows (#2437) (#2522) 2026-07-17 17:20:02 +01:00
CHANGELOG.md perf(hooks): cmdline-first Linux db-lock scan, drop the lsof fallback (#2180) (#2183) 2026-06-13 11:52:14 +01:00
CLAUDE.md feat(ci): review agent runs as a coordinated reviewer swarm (#2572) 2026-07-20 07:31:40 +01:00
compound-engineering.local.md feat: Phase 7 type resolution — return-aware loop inference & PHP class-property iterables (#341) 2026-03-18 08:39:38 +00:00
CONTRIBUTING.md ci: move Node pins to the 22.18 floor 2026-07-21 10:09:34 +00:00
docker-compose.yaml feat(web): support GITNEXUS_BACKEND_URL env var for Docker deployments (#1286) 2026-05-25 11:21:11 +01:00
docker-server.mjs feat(web): support GITNEXUS_BACKEND_URL env var for Docker deployments (#1286) 2026-05-25 11:21:11 +01:00
docker-server.test.mjs feat(web): support GITNEXUS_BACKEND_URL env var for Docker deployments (#1286) 2026-05-25 11:21:11 +01:00
Dockerfile.cli fix(docker): ship runtime-needed published assets (hooks/, skills/) into the image (#2130) (#2132) 2026-06-10 08:38:37 +01:00
Dockerfile.web fix(security): Pin Docker Node base images, remove runtime package-manager CVE surface, verify Trivy on PRs, and harden Dependabot policy (#1455) 2026-05-09 16:55:31 +01:00
DoD.md feat(skills): GitNexus Engineering Tool Kits (#2566) 2026-07-19 15:07:24 +01:00
eslint.config.mjs fix(windows): 32767-char tree-sitter crash + VECTOR extension SIGSEGV (#1433) 2026-05-10 16:00:36 +01:00
GUARDRAILS.md perf(communities): fix the O(communities x N) copy in vendored Leiden, wire Icebug to its real API (#2337) (#2692) 2026-07-25 13:23:17 +01:00
LICENSE docs: update license copyright holder 2026-02-03 22:54:01 +05:30
llms.txt docs: agent development framework, GitHub templates, eval refactor (#479) 2026-03-25 06:48:41 +00:00
MIGRATION.md fix(ingestion): stop double-indexing const X = () => {} as Function + edgeless Const twin (#2687) (#2691) 2026-07-25 16:56:17 +01:00
package-lock.json chore(deps-dev): bump the npm_and_yarn group across 1 directory with 2 updates (#2621) 2026-07-21 22:43:34 +01:00
package.json feat(package): add gitnexus commands for analysis 2026-04-29 16:37:06 +03:00
README.md Merge remote-tracking branch 'upstream/main' 2026-07-23 14:50:09 +08:00
RUNBOOK.md fix(storage): rename index metadata to gitnexus.json with dual-write compatibility (#2363) 2026-07-03 19:32:59 +01:00
SECURITY.md ci(security): add automated security and vulnerability scans (#1297) 2026-05-04 08:21:53 +01:00
skills.mdm FEAT: Added support for optional skill generation based on KuzuDB after initial repo analysis (npx gitnexus analyze --skills) (#171) 2026-03-13 08:29:13 +00:00
swift-ingestion-gaps.md docs: add macro declarations to Swift ingestion gaps 2026-03-23 14:21:32 +01:00
TESTING.md refactor(ingestion): delete legacy call-resolution DAG + heritage processor (RING4-1, #942) (#2023) 2026-06-04 11:07:37 +01:00
type-resolution-roadmap.md feat: implement cross-file binding propagation for multiple languages 2026-03-21 07:47:04 +00:00
type-resolution-system.md feat(ingestion): TypeScript registry-primary scope resolution (Ring 3) (#1050) 2026-04-26 08:23:08 +01:00

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.

abhigyanpatwari%2FGitNexus | Trendshift

Discord npm version License: PolyForm Noncommercial OpenSSF Scorecard CI Workflows

The nervous system for agent context.

Indexes any codebase into a knowledge graph — every dependency, call chain, cluster, and execution flow — then exposes it through smart MCP tools so AI agents never miss code.

💬 Discord · 🌐 Web UI · 🏢 Enterprise (SaaS & self-hosted)

https://github.com/user-attachments/assets/172685ba-8e54-4ea7-9ad1-e31a3398da72

Like DeepWiki, but deeper. DeepWiki helps you understand code. GitNexus lets you analyze it — a knowledge graph tracks every relationship, not just descriptions.

TL;DR: The CLI + MCP makes your AI agent reliable — it gives Cursor, Claude Code, Antigravity, Codex, and friends a deep architectural view of your codebase so they stop missing dependencies, breaking call chains, and shipping blind edits. Even smaller models get full architectural clarity. The Web UI is a quick way to chat with any repo in the browser.

Quick Start

# 1. Index your repo (run from repo root)
npx gitnexus analyze

# 2. Connect your editors (one-time, auto-detects Claude Code, Cursor, Codex, …)
npx gitnexus setup

That's it. analyze indexes the codebase, installs agent skills, registers Claude Code hooks, and creates AGENTS.md / CLAUDE.md context files — all in one command. setup writes the MCP config so your AI agent can use the graph.

Install problems? npm 11 crash · slow cold install · no C++ toolchain

On npm 11.x? npx can crash during install with Cannot destructure property 'package' of 'node.target' (an npm/arborist bug, before GitNexus runs). Use pnpm instead — it builds the native deps explicitly:

pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyze

Or install globally (npm install -g gitnexus@latest) and run gitnexus analyze. See #1939.

Fastest MCP startup: install globally (npm i -g gitnexus) before running gitnexus setup — this writes an absolute-path MCP config that bypasses npx entirely. On a cold cache, an npx-based MCP install can exceed Claude Code's MCP_TIMEOUT default (~30s).

No C++ toolchain? Set GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1 before npm install -g gitnexus to skip the vendored grammar materialize/build for tree-sitter-dart, tree-sitter-proto, tree-sitter-swift, and tree-sitter-kotlin — those four languages won't be parsed, but install completes in seconds without python3/make/g++. Strict =1 only — any other value falls through to the rebuild.

Behind an HTTP proxy / regional firewall? onnxruntime-node's postinstall downloads optional CUDA binaries from api.nuget.org and ignores HTTP_PROXY/HTTPS_PROXY (#2370). The embedding stack is an optional dependency, so a failed download no longer breaks the install — and it self-heals: the first gitnexus analyze --embeddings (or gitnexus embeddings install) fetches the stack through your npm registry config (mirrors/proxies apply, no NuGet) into ~/.gitnexus/embedding-runtime (override with GITNEXUS_EMBEDDING_RUNTIME_DIR). The on-demand prefix needs Node with module.registerHooks (≥ 22.15 on 22.x, ≥ 23.5 on 23.x); on older Node, keep the stack in the install itself with ONNXRUNTIME_NODE_INSTALL=skip npm install -g gitnexus (works on every supported Node).

About tree-sitter-kotlin: like Dart/Proto/Swift, Kotlin is a vendored grammar (under gitnexus/vendor/tree-sitter-kotlin). Upstream ships source only (no prebuilt binaries), so GitNexus cross-builds the platform prebuilds itself (via the build-tree-sitter-prebuilds GitHub Actions workflow) and vendors them — the same uniform pipeline used for Dart, Proto, and Swift. node-gyp-build selects the right .node at require time, so no C/C++ toolchain is needed. If no prebuild matches your platform-arch, only Kotlin (.kt/.kts) parsing is unavailable; the rest of gitnexus is unaffected.

Two Ways to Use GitNexus

CLI + MCP (recommended) Web UI
What Index repos locally, connect AI agents via MCP Visual graph explorer + AI chat in browser
For Daily development with Cursor, Claude Code, Antigravity, Codex, Windsurf, OpenCode Quick exploration, demos, one-off analysis
Scale Full repos, any size Limited by browser memory (~5k files), or unlimited via backend mode
Install npm install -g gitnexus No install — gitnexus.vercel.app
Storage LadybugDB native (fast, persistent) LadybugDB WASM (in-memory, per session)
Parsing Tree-sitter native bindings Tree-sitter WASM
Privacy Everything local, no network Everything in-browser, no server

Bridge mode: gitnexus serve connects the two — the web UI auto-detects the local server and can browse all your CLI-indexed repos without re-uploading or re-indexing.

Why a Knowledge Graph?

Tools like Cursor, Claude Code, Codex, Cline, Roo Code, and Windsurf are powerful — but they don't truly know your codebase structure. So this happens:

  1. AI edits UserService.validate()
  2. Doesn't know 47 functions depend on its return type
  3. Breaking changes ship

Traditional Graph RAG gives the LLM raw graph edges and hopes it explores enough. GitNexus precomputes structure at index time — clustering, tracing, scoring — so tools return complete context in one call:

flowchart TB
    subgraph Traditional["Traditional Graph RAG"]
        direction TB
        U1["User: What depends on UserService?"]
        U1 --> LLM1["LLM receives raw graph"]
        LLM1 --> Q1["Query 1: Find callers"]
        Q1 --> Q2["Query 2: What files?"]
        Q2 --> Q3["Query 3: Filter tests?"]
        Q3 --> Q4["Query 4: High-risk?"]
        Q4 --> OUT1["Answer after 4+ queries"]
    end

    subgraph GN["GitNexus Smart Tools"]
        direction TB
        U2["User: What depends on UserService?"]
        U2 --> TOOL["impact UserService upstream"]
        TOOL --> PRECOMP["Pre-structured response:
        8 callers, 3 clusters, all 90%+ confidence"]
        PRECOMP --> OUT2["Complete answer, 1 query"]
    end

Core innovation: Precomputed Relational Intelligence

  • Reliability — the LLM can't miss context; it's already in the tool response
  • Token efficiency — no 10-query chains to understand one function
  • Model democratization — smaller LLMs work because the tools do the heavy lifting

What Your AI Agent Gets

17 MCP tools (15 per-repo + 2 group)

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

Per-repo tools take an optional repo parameter (omit it when only one repo is indexed) and an optional branch for indexes pinned with gitnexus analyze --branch. Omitting branch queries the workspace index, which follows your checked-out working tree — switching branches and re-running gitnexus analyze updates it incrementally. explain and pdg_query need an index built with gitnexus analyze --pdg.

Resources for instant context

Resource Purpose
gitnexus://repos List all indexed repositories (read this 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

2 MCP prompts for guided workflows

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

Agent skills installed to .claude/skills/ and .agents/skills/ (if .agents/ exists) automatically

  • 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 (--pdg index)
  • Taint Analysis — source→sink data-flow findings (--pdg index)
  • Plan (/gitnexus-plan) — implementation-ready engineering plans backed by the graph and PDG slices
  • Work (/gitnexus-work) — executes a plan as impact-checked, detect_changes-gated atomic commits
  • Review (/gitnexus-review) — graph-backed review of a PR, branch, range, or local diff, with taint pass and per-domain expert lenses
  • LFG (/gitnexus-lfg) — the full pipeline: plan → user gate → work → review

Repo-specific skills — run gitnexus analyze --skills and GitNexus detects the functional areas of your codebase (via Leiden community detection) and generates each one as a direct project skill under .claude/skills/gitnexus-area-<name>/. Each skill describes a module's key files, entry points, execution flows, and cross-area connections, and is regenerated on each --skills run to stay current.

When a repo contains an .agents/ directory, the standard and generated skills are also mirrored to .agents/skills/ (e.g. .agents/skills/gitnexus-cli/, .agents/skills/gitnexus-area-<name>/) so agents that read repo-local .agents/skills/ (like Codex) stay in sync.

Editor Setup

gitnexus setup auto-detects your editors and writes the correct global MCP config. Run it once. To configure only selected integrations, pass --coding-agent/-c with a comma-separated list, e.g. gitnexus setup -c cursor,codex.

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)¹ 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 enrich searches with graph context + PostToolUse hooks that detect a stale index after commits and prompt the agent to reindex.

¹ Antigravity hooks follow the Gemini CLI hooks reference (Antigravity 2.0 is the documented successor to Gemini CLI). Augmentation runs in AfterTool because BeforeTool has no context-injection channel in the Gemini contract — the agent sees graph context appended to the tool result via hookSpecificOutput.additionalContext. Stale-index hints land in the same channel after a successful git commit/merge/rebase/cherry-pick/pull. The schema may evolve if Antigravity-specific hook docs diverge from Gemini CLI's; the implementation will track those changes.

Manual MCP configuration (if you prefer not to run 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

Or via ~/.codex/config.toml (system scope) / .codex/config.toml (project scope):

[mcp_servers.gitnexus]
command = "npx"
args = ["-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 /hooks before they run. Pick one install route (gitnexus setup -c codex or the plugin): plugin hooks load alongside ~/.codex/hooks.json, so installing both can fire duplicate hooks per tool call.

Cursor (~/.cursor/mcp.json — global, works for all projects):

{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}

Antigravity (Google) — ~/.gemini/antigravity/mcp_config.json:

{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}

gitnexus setup also merges an AfterTool entry into ~/.gemini/settings.json (under the canonical Gemini CLI hooks schema) and installs skills to ~/.gemini/antigravity/skills/. Existing user hooks are preserved. The hook adapter's path is rewritten at install time, so run gitnexus setup rather than hand-editing.

OpenCode (~/.config/opencode/config.json):

{
  "mcp": {
    "gitnexus": {
      "type": "local",
      "command": ["gitnexus", "mcp"]
    }
  }
}

CodeBuddy (Tencent) — priority chain, edit the first non-empty file that exists: ~/.codebuddy/.mcp.json (recommended) → ~/.codebuddy/mcp.json (deprecated) → ~/.codebuddy.json (legacy). CodeBuddy reads only the first existing file, so adding servers to a higher-priority file than the one currently in use would hide the servers below it. Create ~/.codebuddy/.mcp.json only if none exist:

{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}

Qoder (Alibaba) — ~/.qoder.json:

{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}
MCP read-only mode

Set GITNEXUS_MCP_READ_ONLY=1 before starting the MCP server to expose only the proven single-repository read surface. Raw cypher, rename and group tools, group routing, and group resources are omitted from discovery and rejected before backend dispatch. Tool descriptions and generated setup/context resources are scrubbed so they do not recommend unavailable routes.

The default is unchanged when the variable is unset or 0. Any other value fails server startup rather than silently weakening the policy.

MCP repository policy

Set GITNEXUS_MCP_ALLOWED_REPOS to a comma-separated list of canonical registry names or absolute indexed paths. Entries are trimmed, resolved against the registry, and deduplicated at startup. When exactly one repository is allowed it becomes the implicit default; when several are allowed, callers must select one unless GITNEXUS_MCP_DEFAULT_REPO is also set.

The default repository must resolve to an allowed repository. Invalid, ambiguous, blank, or mismatched configuration fails startup before stdio or HTTP begins serving. The allowlist applies to tools, aliases, discovery, resources, templates, implicit resolution, and embedded HTTP; hidden repository details are not included in selection errors. Setting only GITNEXUS_MCP_DEFAULT_REPO chooses a default without restricting explicit repository selections. An allowed repository whose name is duplicated in the registry must be configured by path, and its context resource is only served for the unique name form.

MCP response budgets

The query, context, and impact tools accept an optional positive-integer maxTokens argument. It bounds the complete formatted MCP response, including hints and error text, using a deterministic four-UTF-8-bytes-per-token estimate. When truncation is required, the response ends with and remains valid UTF-8.

Set GITNEXUS_MCP_DEFAULT_MAX_TOKENS to apply the same guardrail when callers do not send maxTokens. An explicit tool argument takes precedence. Leaving both unset preserves the existing response byte-for-byte; this is a transport guardrail, not semantic pagination or an exact model-specific tokenizer limit.

CLI Reference

Everyday commands:

gitnexus setup                   # Configure MCP for detected editors (one-time; -c to select)
gitnexus analyze [path]          # Index a repository (or update a stale index)
gitnexus mcp                     # Start MCP server (stdio) — serves all indexed repos
gitnexus serve                   # Start local HTTP server (multi-repo) for web UI connection
gitnexus eval-server             # Start lightweight evaluation HTTP tools (loopback by default)
gitnexus list                    # List all indexed repositories
gitnexus status                  # Show index status for current repo
gitnexus clean                   # Delete index for current repo
gitnexus wiki [path]             # Generate repository wiki from knowledge graph
gitnexus uninstall               # Preview removal of GitNexus MCP/skills/hooks (--force to apply)

You can also query the graph directly from the terminal — gitnexus query, context, impact, trace, cypher, detect-changes, and check mirror the MCP tools of the same names, and gitnexus doctor prints runtime platform capabilities.

Authenticated eval-server binding

gitnexus eval-server binds to 127.0.0.1 by default. Loopback bindings do not require authentication. Any non-loopback bind, including 0.0.0.0, a LAN address, or a hostname that resolves to a LAN IPv4 address, requires GITNEXUS_AUTH_TOKEN. Every endpoint then requires an exact Authorization: Bearer <token> header.

GITNEXUS_AUTH_TOKEN='replace-me' gitnexus eval-server --host 0.0.0.0

The token may be set in the shell, .env.local, or .env in the working directory. Precedence is shell > .env.local > .env. Only GITNEXUS_AUTH_TOKEN is read from those files; their other values are not added to the process environment. Keep token files uncommitted.

All analyze flags
gitnexus analyze --force         # Full rebuild: re-parse + graph rebuild + FTS rebuild
gitnexus analyze --repair-fts    # Fast path: rebuild/verify only FTS indexes on existing index data
gitnexus analyze --skills        # Generate repo-specific skill files from detected communities
gitnexus analyze --skip-embeddings  # Skip embedding generation (faster)
gitnexus analyze --embeddings [limit]  # Enable embedding generation (slower, better search)
gitnexus analyze --skip-agents-md   # Preserve custom AGENTS.md/CLAUDE.md gitnexus section edits
gitnexus analyze --skip-skills      # Skip installing standard skill files under .claude/skills/ and .agents/skills/
gitnexus analyze --skip-git         # Index folders that are not Git repositories
gitnexus analyze --default-branch develop  # Branch used in the generated regression-compare example (base_ref)
gitnexus analyze --verbose       # Log skipped files when parsers are unavailable
gitnexus analyze --worker-timeout 60  # Increase worker idle timeout for slow parses
gitnexus analyze --workers <n>   # Parse worker pool size (>=1; default: cores-1, capped at 16,
                                 # auto-sized to the repo). 0 is rejected — there is no sequential mode.
gitnexus analyze --wal-checkpoint-threshold 67108864  # LadybugDB WAL auto-checkpoint threshold in bytes
                                 # (default 67108864 = 64 MiB; -1 keeps Ladybug stock ~16 MiB)

If analyze reports a worker parse timeout on a large or unusual repository, it keeps running and falls back safely. To give slow worker jobs more time, use --worker-timeout 60 or set GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS=60000. For very large files, GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES controls the worker job byte budget.

Embeddings node limitgitnexus analyze --embeddings generates semantic search vectors with a default 50,000-node safety cap to protect memory on large repositories:

gitnexus analyze --embeddings          # default 50,000 node safety cap
gitnexus analyze --embeddings 0        # disable the cap entirely
gitnexus analyze --embeddings 100000   # custom cap

If embeddings are skipped on a large repository, the indexed graph likely exceeds the default cap — re-run with --embeddings 0 or a higher limit.

Repository groups (multi-repo / monorepo service tracking)
gitnexus group create <name>                           # Create a repository group
gitnexus group add <group> <groupPath> <registryName>  # Add a repo. <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 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
Project config (.gitnexusrc)

Commit a .gitnexusrc JSON file at the repo root to preconfigure recurring analyze options per project, instead of re-passing the same flags every run. It is read from the resolved repo root (not .gitnexus/, which is gitignored index storage). CLI flags always override .gitnexusrc.

{
  // Default branch used in the generated regression-compare example (base_ref).
  // Use this so a project on `develop`/`master` doesn't get "main" rewritten
  // over its fix on every analyze. (Alias: "branch".)
  "defaultBranch": "develop",
  "skipContextFiles": true, // alias of skipAgentsMd: keep your own AGENTS.md/CLAUDE.md
  "skipSkills": true, // don't install standard skill files under .claude/skills/ and .agents/skills/
  "embeddings": true, // generate embeddings by default
  "workerTimeout": 60,
}

A nested analyze block is also accepted (and overrides flat keys for the same option):

{ "analyze": { "defaultBranch": "develop", "skipSkills": true } }

Notes:

  • The default branch is resolved as: --default-branch > .gitnexusrc defaultBranch/branch > auto-detected origin/HEAD > main.
  • skipContextFiles / skipAiContext are aliases for skipAgentsMd — they skip the AGENTS.md / CLAUDE.md block only. They do not imply skipSkills. indexOnly is the stronger option that skips all file injection.
  • Supported keys: defaultBranch (branch), skipAgentsMd (skipContextFiles, skipAiContext), skipSkills, indexOnly, stats/noStats, embeddings, dropEmbeddings, name, allowDuplicateName, maxFileSize, workerTimeout, walCheckpointThreshold, workers, embeddingThreads, embeddingBatchSize, embeddingSubBatchSize, embeddingDevice.
  • The file is JSON only. Unknown keys and invalid values fail fast with an actionable error before analysis starts.
Environment variables

Most analyze knobs are also CLI flags (--workers, --worker-timeout, --max-file-size, --verbose). Use the env-var form when you'd otherwise repeat the same flag every run, or when invoking GitNexus from a long-running host (MCP server, eval-server, CI shell) that already manages its own environment. CLI flags take precedence over env vars; env vars take precedence over built-in defaults.

Variable Default Effect Tune when…
GITNEXUS_WORKER_POOL_SIZE cores - 1, capped at 16 Parse worker pool size (must be ≥ 1). Equivalent to --workers <n>. The worker pool is the sole parse path — there is no sequential parser, so 0 is rejected with an actionable error (the pool self-heals via quarantine + respawn). Constrained containers (cgroup CPU limits) or CI runners with explicit quotas. To narrow down a worker crash set 1 for a single-worker pool — not 0.
GITNEXUS_PARSE_CHUNK_CONCURRENCY 2 Number of chunks whose file contents may be read into memory in parallel while the pool dispatches the current chunk. Worker dispatch itself stays serial. Repos large enough to chunk (multi-MB total source) where disk I/O is a measurable fraction of analyze wall-clock.
GITNEXUS_VERBOSE unset When 1, enables verbose ingestion logs (skipped-file warnings, per-chunk throughput, parse-cache stats). Equivalent to --verbose. Debugging an analyze that "completed" but seems to have missed files; tuning --workers / chunk concurrency against observable throughput.
GITNEXUS_AUTH_TOKEN unset Bearer token required when eval-server binds beyond loopback. May also be read from .env.local or .env; shell values take precedence. Exposing the evaluation HTTP tools to a container, VM, or LAN.
GITNEXUS_PROFILE_DEFERRED unset When 1, emits [deferred-profile] timing/progress logs for the post-chunk deferred resolution band (imports → heritage → buildHeritageMap → legacy call resolution). Implied by GITNEXUS_VERBOSE. Diagnosing analyze stalls in "Resolving calls (all chunks)" on large Java/Kotlin repos (issue #1741) without the full verbose ingestion noise.
GITNEXUS_PROFILE_DEFERRED_SLOW_MS 3000 (verbose) / 5000 Per-file threshold in ms above which processCallsFromExtracted emits a slow file … log line. Parsed via Number(): accepts integers (5000), scientific notation (2.5e3), decimals (.5), and hex (0x10). Non-finite or non-positive values fall back to the default. Hunting a few outlier files dominating the deferred call-resolution stage; lower to surface more, raise to focus only on the worst.
PROF_LBUG_LOAD unset When 1, emits one [lbug-load prof] summary line per loadGraphToLbug call breaking the graph-DB persistence wall into stages (csv-emit / copy-nodes / copy-rels / fallback / total) plus node & edge counts. Zero-cost when unset. Attributing large-repo analyze wall time across CSV generation vs. LadybugDB COPY (issue #2203) — the analyze "emit" timing is the scope-resolution bucket, not this DB-write path.
GITNEXUS_MAX_FILE_SIZE 512 (KB) Walker skip threshold in KB. Hard cap is 32768 (tree-sitter buffer ceiling). Equivalent to --max-file-size <kb>. Indexing repos with intentionally-large source files (generated parsers, vendored bundles) that should still be parsed.
GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS 30000 Worker idle timeout in milliseconds before retry/fallback. Equivalent to --worker-timeout <seconds> × 1000. Slow-parsing files (large minified JS, deeply-nested TS types) that legitimately need more than 30s.
GITNEXUS_WORKER_READY_TIMEOUT_MS 5000 Startup budget in milliseconds for a parse worker to load its grammar bindings and report {type:'ready'}. Slots that miss it are treated as startup crashes. Slow or heavily loaded hosts where a full pool cold-starting concurrently needs more than 5s, and analyze aborts with "did not report ready within 5000ms".
GITNEXUS_FTS_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 for matching repository comments. Re-run gitnexus analyze --repair-fts after changing it. Keyword search quality is poor for non-English comments or identifiers under English stemming.
GITNEXUS_WAL_CHECKPOINT_THRESHOLD 67108864 (64 MiB) LadybugDB WAL auto-checkpoint threshold in bytes. Equivalent to --wal-checkpoint-threshold <bytes>. -1 keeps LadybugDB's stock threshold (~16 MiB). Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments. You need a larger or smaller WAL auto-checkpoint threshold for your analyze workload.
GITNEXUS_LBUG_BUFFER_POOL_SIZE min(2 GiB, 80% RAM) LadybugDB buffer-pool ceiling in bytes for every GitNexus database (analyze, MCP server, serve, group bridges). 0 restores LadybugDB's native unbounded default of 80% of system RAM; invalid values warn and fall back to the default (#2557). During analyze the pool is right-sized to the graph, scaled on non-4 KiB-page hosts 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. A long-lived gitnexus mcp or a big incremental analyze uses too much memory, or a huge repo's working set genuinely needs a pool larger than 2 GiB.
GITNEXUS_LBUG_MAX_DB_SIZE 17179869184 (16 GiB) Maximum size in bytes of a single LadybugDB database file — an mmap/disk-address-space ceiling, not a memory limit (it does not constrain the buffer pool). Invalid values silently fall back to the default. Indexing a genuinely huge monorepo whose on-disk graph index approaches 16 GiB.
GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES 8388608 (8 MB) Per-job byte budget the pool will send to a worker in one postMessage. Very large individual files; mostly diagnostic — bumping past 8 MB risks structured-clone memory pressure.
GITNEXUS_WORKER_MAX_RESPAWNS_PER_SLOT 3 Max replacement spawns per worker slot before the slot is dropped from the active rotation. Bounds respawn loops on a chronically-crashing slot. Hosts where a flaky worker should retry more (raise) or fail-fast (lower) before the slot is dropped.
GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS 5 × subBatchTimeoutMs Total retry wall-time budget per job before quarantining. Combined with timeoutBackoffFactor, prevents exponentially-growing retries from stalling for hours. Slow files that legitimately need long total retry windows; lower to fail-fast on stalls.
GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD max(3, poolSize) Per-slot consecutive deaths before the pool's circuit breaker trips. After tripping, every subsequent dispatch rejects until a fresh pool is created. Hosts where a SIGSEGV-prone native grammar should trip the breaker sooner; CI runners that should fail loudly.
GITNEXUS_WORKER_SHUTDOWN_DRAIN_MS 30000 Max wait at pool shutdown for a retired worker still inside native code. The worker is terminated at its next JS-safe point instead of mid-native-call (which aborts the whole process with Napi::Error, #2432); on expiry it is left running, unref'd, and terminated when it surfaces. Shutdown latency matters more than draining a wedged worker (lower), or a legitimately-slow native grammar needs longer to surface (raise).
GITNEXUS_CPP_CAPTURE_BUDGET_MS 20000 Per-file wall-clock budget for C++ capture extraction. On breach the file keeps the captures accumulated so far and logs a warning — the worker returns to JS instead of stalling in native-heavy loops (#2432). 0 expires immediately. Pathological generated C++ that still exceeds the budget after the indexed lookups; raise for completeness, lower to fail-fast.
GITNEXUS_CHUNK_BYTE_BUDGET 2097152 (2 MB) Chunk boundary used for cache-key composition and dispatch. Smaller = finer-grained cache hits but more dispatch overhead. Tuning incremental-analyze cache behavior on monorepos.
GITNEXUS_NO_GITIGNORE unset When set, skips .gitignore parsing. .gitnexusignore is still honored. Indexing a repo whose .gitignore excludes files you actually want indexed (e.g., generated code committed for cross-repo lookup).
GITNEXUS_SKIP_OPTIONAL_GRAMMARS unset When =1 strictly, skips the vendored grammar materialize for tree-sitter-dart, tree-sitter-proto, tree-sitter-swift, and tree-sitter-kotlin at install time (and the Dart/Proto source builds). Those four won't be parsed; the install still succeeds. Installing on a host without a C++ toolchain or where the vendored prebuilds don't match; willing to skip Dart/Proto/Swift/Kotlin parsing.
GITNEXUS_MCP_READ_ONLY unset Set to 1 to expose only proven single-repository read tools and resources; 0 disables the policy and any other value fails startup. The MCP server runs in an environment where graph mutation, raw Cypher, and cross-repository group routing must be unavailable.
GITNEXUS_MCP_ALLOWED_REPOS unset Comma-separated allowlist of canonical indexed repository names or absolute paths. Invalid, ambiguous, or blank entries fail startup. One MCP process must expose only a bounded subset of the repositories in the global registry.
GITNEXUS_MCP_DEFAULT_REPO unset Canonical indexed repository name or absolute path used when a tool or resource omits its repository. Must belong to the allowlist when one is set. Several repositories are available but unqualified MCP calls should resolve deterministically.
GITNEXUS_MCP_DEFAULT_MAX_TOKENS unset Default positive-integer response budget for MCP query, context, and impact, estimated at four UTF-8 bytes per token. Explicit maxTokens wins. Long MCP responses consume too much model context and callers cannot reliably add a per-request budget.
gitnexus uninstall

gitnexus uninstall reverses gitnexus 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 --force to apply. Per-repo indexes (gitnexus clean --all) and the global npm package (npm uninstall -g gitnexus) are left for you to remove.

Publishing to understand-quickly (opt-in)

looptech-ai/understand-quickly is a public registry of code-knowledge graphs that lists gitnexus@1 as a first-class format. After registering your repo once (npx @understand-quickly/cli add or the wizard), gitnexus publish fires a single repository_dispatch event so the registry resyncs your entry on demand instead of waiting for the nightly job.

It is opt-in and a no-op without UNDERSTAND_QUICKLY_TOKEN — a fine-grained GitHub PAT with Repository dispatches: write on the registry repo. Nothing else happens; no graph file is uploaded. See the protocol spec for the full contract.

How It Works

GitNexus builds a complete knowledge graph of your codebase through a multi-phase indexing pipeline:

  1. Structure — walks the file tree and maps folder/file relationships
  2. Parsing — extracts functions, classes, methods, and interfaces using Tree-sitter ASTs
  3. Resolution — resolves imports, function calls, heritage, constructor inference, and self/this receiver types across files with language-aware logic
  4. Clustering — groups related symbols into functional communities
  5. Processes — traces execution flows from entry points through call chains
  6. Search — builds hybrid search indexes for fast retrieval

Supported Languages

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 Bindingsimport { 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

Control flow (CFG, opt-in --pdg) — per-function control-flow graphs (BasicBlock nodes + CFG edges) feeding the PDG/taint substrate, currently TypeScript & JavaScript (#2081 M1); other languages planned. Off by default.

Multi-Repo Architecture

GitNexus uses a global registry so one MCP server can serve multiple indexed repos. No per-project MCP config needed — set it up once and it works everywhere.

Each gitnexus analyze stores the index in .gitnexus/ inside the repo (portable, gitignored) and registers a pointer in ~/.gitnexus/registry.json. When an AI agent starts, the MCP server reads the registry and can serve any indexed repo. LadybugDB connections are opened lazily on first query and evicted after 5 minutes of inactivity (max 5 concurrent). If only one repo is indexed, the repo parameter is optional on all tools — agents don't need to change anything.

Architecture diagram
flowchart TD
    subgraph CLI [CLI Commands]
        Setup["gitnexus setup"]
        Analyze["gitnexus analyze"]
        Clean["gitnexus clean"]
        List["gitnexus list"]
    end

    subgraph Registry ["~/.gitnexus/"]
        RegFile["registry.json"]
    end

    subgraph Repos [Project Repos]
        RepoA[".gitnexus/ in repo A"]
        RepoB[".gitnexus/ in repo B"]
    end

    subgraph MCP [MCP Server]
        Server["server.ts"]
        Backend["LocalBackend"]
        Pool["Connection Pool"]
        ConnA["LadybugDB conn A"]
        ConnB["LadybugDB conn B"]
    end

    Setup -->|"writes global MCP config"| CursorConfig["~/.cursor/mcp.json"]
    Analyze -->|"registers repo"| RegFile
    Analyze -->|"stores index"| RepoA
    Clean -->|"unregisters repo"| RegFile
    List -->|"reads"| RegFile
    Server -->|"reads registry"| RegFile
    Server --> Backend
    Backend --> Pool
    Pool -->|"lazy open"| ConnA
    Pool -->|"lazy open"| ConnB
    ConnA -->|"queries"| RepoA
    ConnB -->|"queries"| RepoB

Tool Examples

Impact Analysis

impact({target: "UserService", direction: "upstream", minConfidence: 0.8})

TARGET: Class UserService (src/services/user.ts)

UPSTREAM (what depends on this):
  Depth 1 (WILL BREAK):
    handleLogin [CALLS 90%] -> src/api/auth.ts:45
    handleRegister [CALLS 90%] -> src/api/auth.ts:78
    UserController [CALLS 85%] -> src/controllers/user.ts:12
  Depth 2 (LIKELY AFFECTED):
    authRouter [IMPORTS] -> src/routes/auth.ts

Options: maxDepth, minConfidence, relationTypes (CALLS, IMPORTS, EXTENDS, IMPLEMENTS), includeTests, limit (max symbols per depth, default 100), offset (pagination start per depth), summaryOnly (counts and risk only, omits symbol list)

Disambiguation — when several symbols share the target name, impact returns a ranked ambiguous candidate list instead of guessing. Narrow it with target_uid (exact, zero-ambiguity), file_path, or kind (Function, Class, Method, …). From the CLI these are --uid, --file, and --kind, matching gitnexus context:

gitnexus impact get_embeddings                       # → ambiguous: lists ranked candidates
gitnexus impact get_embeddings --file src/embed.py   # → resolves to the one in that file
gitnexus impact get_embeddings --uid "Function:src/embed.py:get_embeddings"  # exact
More examples: search · context · detect_changes · rename · Cypher
query({search_query: "authentication middleware"})

processes:
  - summary: "LoginFlow"
    priority: 0.042
    symbol_count: 4
    process_type: cross_community
    step_count: 7

process_symbols:
  - name: validateUser
    type: Function
    filePath: src/auth/validate.ts
    process_id: proc_login
    step_index: 2

definitions:
  - name: AuthConfig
    type: Interface
    filePath: src/types/auth.ts

Context (360-degree Symbol View)

context({name: "validateUser"})

symbol:
  uid: "Function:validateUser"
  kind: Function
  filePath: src/auth/validate.ts
  startLine: 15

incoming:
  calls: [handleLogin, handleRegister, UserController]
  imports: [authRouter]

outgoing:
  calls: [checkPassword, createSession]

processes:
  - name: LoginFlow (step 2/7)
  - name: RegistrationFlow (step 3/5)

Detect Changes (Pre-Commit)

detect_changes({scope: "all"})

summary:
  changed_count: 12
  affected_count: 3
  changed_files: 4
  risk_level: medium

changed_symbols: [validateUser, AuthService, ...]
affected_processes: [LoginFlow, RegistrationFlow, ...]

Rename (Multi-File)

rename({symbol_name: "validateUser", new_name: "verifyUser", dry_run: true})

status: success
files_affected: 5
total_edits: 8
graph_edits: 6     (high confidence)
text_search_edits: 2  (review carefully)
changes: [...]

Cypher Queries

-- Find what calls auth functions with high confidence
MATCH (c:Community {heuristicLabel: 'Authentication'})<-[:CodeRelation {type: 'MEMBER_OF'}]-(fn)
MATCH (caller)-[r:CodeRelation {type: 'CALLS'}]->(fn)
WHERE r.confidence > 0.8
RETURN caller.name, fn.name, r.confidence
ORDER BY r.confidence DESC

Wiki Generation

Generate LLM-powered documentation from your knowledge graph:

# Requires an LLM API key (OPENAI_API_KEY, etc.)
gitnexus wiki

# Use a custom model or provider (default model: minimax/minimax-m2.5)
gitnexus wiki --model gpt-4o
gitnexus wiki --base-url https://api.anthropic.com/v1

# Force full regeneration
gitnexus wiki --force

# Increase the timeout or retries for large codebases or slow LLM providers
gitnexus wiki --timeout <seconds>  # LLM request timeout in seconds (default: disabled)
gitnexus wiki --retries <n>        # Max LLM retry attempts per request (default: 3)

# Allow a specific LAN/self-hosted HTTP LLM host (HTTPS is preferred for remote endpoints)
gitnexus wiki --base-url http://llama-box.local:8080/v1 --allow-insecure-connection llama-box.local
# Or set a comma-separated host allowlist:
GITNEXUS_ALLOW_INSECURE_CONNECTION=llama-box.local,192.168.1.23

# Change the output language
gitnexus wiki --lang <lang>  # e.g. english, chinese, spanish, japanese

For safety, http:// LLM base URLs are allowed by default only for loopback hosts (localhost, 127.0.0.1, ::1). --allow-insecure-connection and GITNEXUS_ALLOW_INSECURE_CONNECTION accept exact hostnames or IP addresses only; do not include schemes, ports, paths, credentials, or wildcards.

The wiki generator reads the indexed graph structure, groups files into modules via LLM, generates per-module documentation pages, and creates an overview page — all with cross-references to the knowledge graph.

Web UI (browser-based)

A client-side graph explorer and AI chat — your code never leaves your machine.

Try it now: gitnexus.vercel.app — run npx gitnexus@latest serve locally and the page auto-connects to your local backend.

gitnexus_img

The web UI uses the same indexing pipeline as the CLI but runs entirely in WebAssembly (Tree-sitter WASM, LadybugDB WASM, in-browser embeddings). It's great for quick exploration but limited by browser memory for larger repos.

Local Backend Mode: run gitnexus serve and open the web UI — it auto-detects the server and shows all your indexed repos, with full AI chat support. No re-upload, no re-index. The agent's tools (Cypher queries, search, code navigation) route through the backend HTTP API automatically.

Run the frontend locally
git clone https://github.com/abhigyanpatwari/gitnexus.git
cd gitnexus/gitnexus-shared && npm install && npm run build
cd ../gitnexus-web && npm install
npm run dev
# Then in another terminal, start the backend the frontend connects to:
npx gitnexus@latest serve

Docker

docker compose up -d

This starts the server on http://localhost:4747 and the web UI on http://localhost:4173. The UI auto-detects the server because the browser runs on the host and reaches the container via the mapped port.

The official setup ships two signed images, published identically to GitHub Container Registry (GHCR) and Docker Hub — same build, same digest, same Cosign signature:

Purpose GHCR (default in docker-compose.yaml) Docker Hub mirror
CLI / gitnexus serve backend (HTTP API on port 4747, MCP, indexer) ghcr.io/abhigyanpatwari/gitnexus:latest akonlabs/gitnexus:latest
Static web UI (port 4173) ghcr.io/abhigyanpatwari/gitnexus-web:latest akonlabs/gitnexus-web:latest

A named volume (gitnexus-data) persists the global registry, indexes, and cloned repos at /data/gitnexus inside the server container. To make repos on your host machine indexable, set WORKSPACE_DIR before bringing the stack up:

WORKSPACE_DIR=$HOME/code docker compose up -d
# Inside the server container the directory is mounted read-only at /workspace.
docker compose exec gitnexus-server gitnexus index /workspace/my-repo

Heads-up — image rename. Earlier releases published the web UI under ghcr.io/abhigyanpatwari/gitnexus. That slug now hosts the CLI/server image and the UI moved to ghcr.io/abhigyanpatwari/gitnexus-web. Previous tags remain pullable, but new versions are only published under the new slugs — update your docker run / compose files (or just adopt the bundled compose).

Direct docker run & env file
# Server
docker run --rm -d \
  --name gitnexus-server \
  -p 4747:4747 \
  -v gitnexus-data:/data/gitnexus \
  ghcr.io/abhigyanpatwari/gitnexus:latest

# Web UI
docker run --rm -d \
  --name gitnexus-web \
  -p 4173:4173 \
  ghcr.io/abhigyanpatwari/gitnexus-web:latest

Optional env file (override image tags, container names, ports, workspace dir):

cp .env.example .env
docker compose --env-file .env up -d

Files:

  • Dockerfile.web — builds gitnexus-shared and gitnexus-web, then serves the production frontend.
  • Dockerfile.cli — builds the CLI/server (with its native deps) and runs gitnexus serve --host 0.0.0.0.
  • docker-compose.yaml — starts both signed images side by side.
  • .env.example — overrides for image names, container names, ports, and the workspace mount.
Versioning & supply-chain protection (Cosign signatures, provenance, Kubernetes admission policy)

The Docker images are version-locked to the npm package:

  • Stable images are only published from vX.Y.Z git tags (via docker.yml triggered directly by the tag push), and the workflow refuses to build unless the tag exactly matches gitnexus/package.json's version. So ghcr.io/abhigyanpatwari/gitnexus:1.6.2 (and its Docker Hub mirror akonlabs/gitnexus:1.6.2) is byte-for-byte the same release as npm install gitnexus@1.6.2 — no drift, no floating builds from main. Both registries receive the same digest from a single build step, so you can pull from either and the signature verifies identically.
  • Release-candidate images (e.g. :1.7.0-rc.1) are published alongside each RC npm release. They are built by publish.yml calling docker.yml as a reusable workflow after the RC tag is created and pushed.
  • :latest is auto-promoted only from non-prerelease tags by the Docker metadata action, so it always points at a real, npm-published version.

Both images are signed with Cosign keyless signing using the workflow's GitHub OIDC identity, and shipped with build provenance and SBOM attestations. This is your protection against supply-chain attacks: even if an attacker republishes a same-named image elsewhere (or somehow pushes to a typo-squatted registry), they cannot forge a Cosign signature tied to abhigyanpatwari/GitNexus's docker.yml. Always verify before pulling into sensitive environments.

Stable releases — signed from the v* tag ref:

cosign verify ghcr.io/abhigyanpatwari/gitnexus:1.6.2 \
  --certificate-identity-regexp '^https://github\.com/abhigyanpatwari/GitNexus/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$' \
  --certificate-oidc-issuer https://token.actions.githubusercontent.com

# Same signature verifies the Docker Hub mirror (identical digest):
cosign verify docker.io/akonlabs/gitnexus:1.6.2 \
  --certificate-identity-regexp '^https://github\.com/abhigyanpatwari/GitNexus/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$' \
  --certificate-oidc-issuer https://token.actions.githubusercontent.com

The regex pins the certificate identity to this repo's docker.yml workflow run from a v* tag — rejecting unsigned images, images signed by other workflows, and images signed from unprotected refs. It is identical for both registries because both sets of tags were signed at the same digest in one workflow run.

Release candidates — signed from refs/heads/main (the caller's ref when publish.yml invokes docker.yml as a reusable workflow):

cosign verify ghcr.io/abhigyanpatwari/gitnexus:1.7.0-rc.1 \
  --certificate-identity 'https://github.com/abhigyanpatwari/GitNexus/.github/workflows/docker.yml@refs/heads/main' \
  --certificate-oidc-issuer https://token.actions.githubusercontent.com

You can also inspect the build provenance and SBOM:

cosign download attestation ghcr.io/abhigyanpatwari/gitnexus:1.6.2 \
  --predicate-type https://slsa.dev/provenance/v1

Kubernetes: enforce signatures at admission. Ship the bundled ClusterImagePolicy so the Sigstore policy-controller rejects any GitNexus pod whose image is not signed by this repo's docker.yml running from a vX.Y.Z tag — the same identity the cosign verify snippet above pins.

# 1. Install the controller (one-time, cluster-wide)
helm repo add sigstore https://sigstore.github.io/helm-charts && helm repo update
helm install policy-controller -n cosign-system --create-namespace \
  sigstore/policy-controller

# 2. Opt your namespace in
kubectl label namespace <your-ns> policy.sigstore.dev/include=true

# 3. Apply the policy
kubectl apply -f deploy/kubernetes/cluster-image-policy.yaml

After this, attempting to deploy an unsigned image — or one signed by anything other than abhigyanpatwari/GitNexus's docker.yml at a v* tag — fails the admission webhook before a pod is ever created. This turns the verifiable signature into an enforced policy, which is the supply-chain control most clusters actually need.

Enterprise

GitNexus is available as an enterprise offering — fully managed SaaS or self-hosted deployment. Commercial use of the OSS version is also available with proper licensing.

Enterprise includes:

  • PR Review — automated blast radius analysis on pull requests
  • Auto-updating Code Wiki — always up-to-date documentation (Code Wiki is also available in OSS)
  • Auto-reindexing — knowledge graph stays fresh automatically
  • Multi-repo support — unified graph across repositories
  • OCaml support — additional language coverage
  • Priority feature/language support — request new languages or features

Upcoming: auto regression forensics · end-to-end test generation

👉 Learn more at akonlabs.com — for commercial licensing or enterprise inquiries, ping us on Discord or email founders@akonlabs.com

Community Integrations

Built by the community — not officially maintained, but worth checking out.

Project Author Description
pi-gitnexus @tintinweb GitNexus plugin for pipi install npm:pi-gitnexus
gitnexus-stable-ops @ShunsukeHayashi Stable ops & deployment workflows (Miyabi ecosystem)
KiloCode MCP workflow @oktanishq Guide to connect GitNexus MCP to Kilo Code and verify tools.

Have a project built on GitNexus? Open a PR to add it here!

Roadmap

Actively building:

  • LLM Cluster Enrichment — semantic cluster names via LLM API
  • AST Decorator Detection — parse @Controller, @Get, etc.
  • Incremental Indexing — only re-index changed files

Recently completed:

  • Constructor-Inferred Type Resolution, self/this Receiver Mapping
  • Wiki Generation, Multi-File Rename, Git-Diff Impact Analysis
  • Process-Grouped Search, 360-Degree Context, Claude Code Hooks
  • Multi-Repo MCP, Zero-Config Setup, 14 Language Support
  • Community Detection, Process Detection, Confidence Scoring
  • Hybrid Search, Vector Index

Development

  • ARCHITECTURE.md — packages, index → graph → MCP flow, where to change code
  • RUNBOOK.md — analyze, embeddings, stale index, MCP recovery, CI snippets
  • GUARDRAILS.md — safety rules and operational "Signs" for contributors and agents
  • CONTRIBUTING.md — license, setup, commits, and pull requests
  • TESTING.md — test commands for gitnexus and gitnexus-web

Tech Stack

Layer CLI Web
Runtime Node.js (native) Browser (WASM)
Parsing Tree-sitter native bindings Tree-sitter WASM
Database LadybugDB native LadybugDB WASM
Embeddings HuggingFace transformers.js (GPU/CPU) transformers.js (WebGPU/WASM)
Search BM25 + semantic + RRF BM25 + semantic + RRF
Agent Interface MCP (stdio) LangChain ReAct agent
Visualization Sigma.js + Graphology (WebGL)
Frontend React 18, TypeScript, Vite, Tailwind v4
Clustering Graphology Graphology
Concurrency Worker threads + async Web Workers + Comlink

Security & Privacy

  • CLI: everything runs locally on your machine. No network calls. Index stored in .gitnexus/ (gitignored). Global registry at ~/.gitnexus/ stores only paths and metadata.
  • Web: everything runs in your browser. No code uploaded to any server. API keys stored in localStorage only.
  • Open source — audit the code yourself.

Star History

Star History Chart

Acknowledgments