gitnexus 1.6.3-rc.8 → 1.6.3

package/dist/_shared/scope-resolution/resolve-type-ref.d.ts

@@ -36,18 +36,9 @@
  * Pure function — safe to call repeatedly; no side effects.
  */
 import type { SymbolDefinition } from './symbol-definition.js';
-import type { Scope, ScopeId, TypeRef } from './types.js';
+import type { ScopeLookup, TypeRef } from './types.js';
 import type { DefIndex } from './def-index.js';
 import type { QualifiedNameIndex } from './qualified-name-index.js';
-/**
- * Minimal scope-lookup contract required by `resolveTypeRef`. Implemented by
- * the `ScopeTree` from #912; declared here so #916 can ship as a standalone
- * piece without a hard dependency on the full scope-tree implementation. Any
- * structure that hands back a `Scope` by `ScopeId` satisfies this contract.
- */
-export interface ScopeLookup {
-    getScope(id: ScopeId): Scope | undefined;
-}
 /**
  * All inputs `resolveTypeRef` needs from the semantic model. Bundled into a
  * context object so the call site stays short and the interface is stable as

package/dist/_shared/scope-resolution/resolve-type-ref.d.ts.map

@@ -1 +1 @@
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package/dist/_shared/scope-resolution/resolve-type-ref.js

@@ -51,6 +51,12 @@ const STRICT_ORIGINS = new Set([
  * container, not a value type. `Function` / `Method` / `Variable` are
  * excluded by design: a `rawName` bound to them at a strict origin is a
  * *shadowing* binding, which the algorithm short-circuits to `null`.
+ *
+ * `'Type'` (the generic `NodeLabel` value) is also excluded — verified
+ * against `gitnexus/src/core/ingestion/` at the time of writing, no
+ * production extractor emits `type: 'Type'` for annotation-relevant
+ * symbols. Should a future extractor start emitting it, add `'Type'`
+ * here and add a test asserting the new path.
  */
 const TYPE_KINDS = new Set([
     'Class',

package/dist/_shared/scope-resolution/resolve-type-ref.js.map

@@ -1 +1 @@
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package/dist/_shared/scope-resolution/scope-tree.d.ts

@@ -18,14 +18,14 @@
  *     pointers would be a category error — a `File` scope is not the
  *     parent of another file's scopes; imports do that job.)
  *
- * Satisfies the `ScopeLookup` contract from #916 (`resolve-type-ref`), so
- * `resolveTypeRef` can take a `ScopeTree` directly without adapters.
+ * Satisfies the `ScopeLookup` contract (defined in `./types.js`), so
+ * `resolveTypeRef` (#916) and the scope-aware registries (#917) can take a
+ * `ScopeTree` directly without adapters.
  *
  * Immutable surface: `byId` is a `ReadonlyMap`; children arrays are
  * `Object.freeze`d; miss lookups return a shared frozen empty array.
  */
-import type { Scope, ScopeId } from './types.js';
-import type { ScopeLookup } from './resolve-type-ref.js';
+import type { Scope, ScopeId, ScopeLookup } from './types.js';
 export interface ScopeTree extends ScopeLookup {
     readonly size: number;
     readonly byId: ReadonlyMap<ScopeId, Scope>;

package/dist/_shared/scope-resolution/scope-tree.d.ts.map

@@ -1 +1 @@
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package/dist/_shared/scope-resolution/scope-tree.js

@@ -18,8 +18,9 @@
  *     pointers would be a category error — a `File` scope is not the
  *     parent of another file's scopes; imports do that job.)
  *
- * Satisfies the `ScopeLookup` contract from #916 (`resolve-type-ref`), so
- * `resolveTypeRef` can take a `ScopeTree` directly without adapters.
+ * Satisfies the `ScopeLookup` contract (defined in `./types.js`), so
+ * `resolveTypeRef` (#916) and the scope-aware registries (#917) can take a
+ * `ScopeTree` directly without adapters.
  *
  * Immutable surface: `byId` is a `ReadonlyMap`; children arrays are
  * `Object.freeze`d; miss lookups return a shared frozen empty array.

package/dist/_shared/scope-resolution/scope-tree.js.map

@@ -1 +1 @@
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+{"version":3,"file":"scope-tree.js","sourceRoot":"","sources":["../../src/scope-resolution/scope-tree.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AAuBH,+EAA+E;AAE/E;;;;GAIG;AACH,MAAM,OAAO,uBAAwB,SAAQ,KAAK;IAErC;IADX,YACW,SAMe,EACxB,OAAe;QAEf,KAAK,CAAC,OAAO,CAAC,CAAC;QATN,cAAS,GAAT,SAAS,CAMM;QAIxB,IAAI,CAAC,IAAI,GAAG,yBAAyB,CAAC;IACxC,CAAC;CACF;AAED,8EAA8E;AAE9E;;;;;;GAMG;AACH,MAAM,UAAU,cAAc,CAAC,MAAwB;IACrD,MAAM,IAAI,GAAG,IAAI,GAAG,EAAkB,CAAC;IACvC,MAAM,YAAY,GAAG,IAAI,GAAG,EAAsB,CAAC;IAEnD,yEAAyE;IACzE,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,CAAC;YACvB,MAAM,IAAI,uBAAuB,CAC/B,oBAAoB,EACpB,wBAAwB,KAAK,CAAC,EAAE,uCAAuC,CACxE,CAAC;QACJ,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,CAAC,CAAC;IAC5B,CAAC;IAED,yEAAyE;IACzE,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,KAAK,CAAC,MAAM,KAAK,IAAI,EAAE,CAAC;YAC1B,IAAI,KAAK,CAAC,IAAI,KAAK,QAAQ,EAAE,CAAC;gBAC5B,MAAM,IAAI,uBAAuB,CAC/B,4BAA4B,EAC5B,UAAU,KAAK,CAAC,EAAE,eAAe,KAAK,CAAC,IAAI,0DAA0D,CACtG,CAAC;YACJ,CAAC;YACD,SAAS;QACX,CAAC;QAED,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QACtC,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,MAAM,IAAI,uBAAuB,CAC/B,kBAAkB,EAClB,UAAU,KAAK,CAAC,EAAE,wBAAwB,KAAK,CAAC,MAAM,mCAAmC,CAC1F,CAAC;QACJ,CAAC;QACD,IAAI,MAAM,CAAC,QAAQ,KAAK,KAAK,CAAC,QAAQ,EAAE,CAAC;YACvC,MAAM,IAAI,uBAAuB,CAC/B,4BAA4B,EAC5B,UAAU,KAAK,CAAC,EAAE,MAAM,KAAK,CAAC,QAAQ,iBAAiB,MAAM,CAAC,EAAE,0BAA0B,MAAM,CAAC,QAAQ,6CAA6C,CACvJ,CAAC;QACJ,CAAC;QACD,IAAI,CAAC,qBAAqB,CAAC,MAAM,CAAC,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;YACtD,MAAM,IAAI,uBAAuB,CAC/B,2BAA2B,EAC3B,iBAAiB,MAAM,CAAC,EAAE,QAAQ,WAAW,CAAC,MAAM,CAAC,KAAK,CAAC,qCAAqC,KAAK,CAAC,EAAE,QAAQ,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAC5I,CAAC;QACJ,CAAC;QAED,IAAI,MAAM,GAAG,YAAY,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;QACzC,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,MAAM,GAAG,EAAE,CAAC;YACZ,YAAY,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,EAAE,MAAM,CAAC,CAAC;QACtC,CAAC;QACD,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACxB,CAAC;IAED,yEAAyE;IACzE,KAAK,MAAM,CAAC,QAAQ,EAAE,QAAQ,CAAC,IAAI,YAAY,EAAE,CAAC;QAChD,IAAI,QAAQ,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QAClC,oEAAoE;QACpE,mCAAmC;QACnC,MAAM,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAE,CAAC,CAAC,KAAK,EAAE,CAAC;QAC7D,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,eAAe,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC;QAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YACzC,MAAM,IAAI,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC;YAC9B,MAAM,IAAI,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC;YAC1B,IAAI,aAAa,CAAC,IAAI,CAAC,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBAC1C,MAAM,IAAI,uBAAuB,CAC/B,wBAAwB,EACxB,gCAAgC,QAAQ,eAAe,IAAI,CAAC,EAAE,KAAK,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,IAAI,CAAC,EAAE,KAAK,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAC1I,CAAC;YACJ,CAAC;QACH,CAAC;IACH,CAAC;IAED,4DAA4D;IAC5D,MAAM,cAAc,GAAG,IAAI,GAAG,EAA+B,CAAC;IAC9D,KAAK,MAAM,CAAC,QAAQ,EAAE,QAAQ,CAAC,IAAI,YAAY,EAAE,CAAC;QAChD,cAAc,CAAC,GAAG,CAAC,QAAQ,EAAE,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC;IAChE,CAAC;IAED,OAAO,UAAU,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;AAC1C,CAAC;AAED,+EAA+E;AAE/E,MAAM,cAAc,GAAuB,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;AAE7D,SAAS,UAAU,CACjB,IAAyB,EACzB,YAA8C;IAE9C,OAAO;QACL,IAAI;QACJ,IAAI,IAAI;YACN,OAAO,IAAI,CAAC,IAAI,CAAC;QACnB,CAAC;QACD,QAAQ,CAAC,EAAW;YAClB,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACtB,CAAC;QACD,SAAS,CAAC,EAAW;YACnB,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;YAC3B,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,CAAC,MAAM,KAAK,IAAI;gBAAE,OAAO,SAAS,CAAC;YACnE,OAAO,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAChC,CAAC;QACD,WAAW,CAAC,EAAW;YACrB,OAAO,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,cAAc,CAAC;QAChD,CAAC;QACD,YAAY,CAAC,EAAW;YACtB,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;YAC3B,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,CAAC,MAAM,KAAK,IAAI;gBAAE,OAAO,cAAc,CAAC;YACxE,MAAM,GAAG,GAAc,EAAE,CAAC;YAC1B,MAAM,OAAO,GAAG,IAAI,GAAG,CAAU,CAAC,EAAE,CAAC,CAAC,CAAC;YACvC,IAAI,MAAM,GAAmB,KAAK,CAAC,MAAM,CAAC;YAC1C,OAAO,MAAM,KAAK,IAAI,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC;gBAC/C,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;gBACpB,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;gBACjB,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;gBAC9B,MAAM,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC;YACnD,CAAC;YACD,OAAO,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QAC5B,CAAC;QACD,GAAG,CAAC,EAAW;YACb,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACtB,CAAC;KACF,CAAC;AACJ,CAAC;AAED;;;;;GAKG;AACH,SAAS,qBAAqB,CAAC,KAAY,EAAE,KAAY;IACvD,IACE,KAAK,CAAC,SAAS,KAAK,KAAK,CAAC,SAAS;QACnC,KAAK,CAAC,QAAQ,KAAK,KAAK,CAAC,QAAQ;QACjC,KAAK,CAAC,OAAO,KAAK,KAAK,CAAC,OAAO;QAC/B,KAAK,CAAC,MAAM,KAAK,KAAK,CAAC,MAAM,EAC7B,CAAC;QACD,OAAO,KAAK,CAAC;IACf,CAAC;IACD,MAAM,qBAAqB,GACzB,KAAK,CAAC,SAAS,GAAG,KAAK,CAAC,SAAS;QACjC,CAAC,KAAK,CAAC,SAAS,KAAK,KAAK,CAAC,SAAS,IAAI,KAAK,CAAC,QAAQ,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC;IAC5E,MAAM,kBAAkB,GACtB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO;QAC7B,CAAC,KAAK,CAAC,OAAO,KAAK,KAAK,CAAC,OAAO,IAAI,KAAK,CAAC,MAAM,IA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package/dist/_shared/scope-resolution/shadow/aggregate.d.ts

@@ -5,11 +5,16 @@
  * Pure functions; no I/O. The harness persists per-run JSON; the dashboard
  * reads `.gitnexus/shadow-parity/latest.json` and renders.
  *
+ * Related types — `ShadowAgreement`, `ShadowCallsite`, `ShadowDiff` — are
+ * defined alongside `diffResolutions` in `./diff.ts` and re-exported
+ * through the top-level `gitnexus-shared` barrel. Consumers import all
+ * three from `gitnexus-shared`, not from this module.
+ *
  * Part of RFC #909 Ring 2 SHARED — #918.
  */
 import type { SupportedLanguages } from '../../languages.js';
 import type { ResolutionEvidence } from '../types.js';
-import type { ShadowAgreement, ShadowDiff } from './diff.js';
+import type { ShadowDiff } from './diff.js';
 export interface LanguageParityRow {
     readonly language: SupportedLanguages;
     readonly totalCalls: number;
@@ -55,5 +60,4 @@ export declare function aggregateDiffs(diffs: readonly {
     readonly language: SupportedLanguages;
     readonly diff: ShadowDiff;
 }[], now?: Date): ShadowParityReport;
-export type { ShadowAgreement, ShadowDiff };
 //# sourceMappingURL=aggregate.d.ts.map

package/dist/_shared/scope-resolution/shadow/aggregate.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"aggregate.d.ts","sourceRoot":"","sources":["../../../src/scope-resolution/shadow/aggregate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAC7D,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,aAAa,CAAC;AACtD,OAAO,KAAK,EAAmB,UAAU,EAAE,MAAM,WAAW,CAAC;AAI7D,MAAM,WAAW,iBAAiB;IAChC,QAAQ,CAAC,QAAQ,EAAE,kBAAkB,CAAC;IACtC,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B;;;;;;;;OAQG;IACH,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;IACxB;;;;OAIG;IACH,QAAQ,CAAC,iBAAiB,EAAE,WAAW,CAAC,kBAAkB,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC,CAAC;CAC7E;AAED,MAAM,WAAW,kBAAkB;IACjC,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,QAAQ,CAAC,WAAW,EAAE,SAAS,iBAAiB,EAAE,CAAC;IACnD,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,iBAAiB,EAAE,UAAU,GAAG,mBAAmB,CAAC,CAAC;CAC7E;AAID;;;;;;;;;;GAUG;AACH,wBAAgB,cAAc,CAC5B,KAAK,EAAE,SAAS;IAAE,QAAQ,CAAC,QAAQ,EAAE,kBAAkB,CAAC;IAAC,QAAQ,CAAC,IAAI,EAAE,UAAU,CAAA;CAAE,EAAE,EACtF,GAAG,GAAE,IAAiB,GACrB,kBAAkB,CAuBpB"}

package/dist/_shared/scope-resolution/shadow/aggregate.js

@@ -5,6 +5,11 @@
  * Pure functions; no I/O. The harness persists per-run JSON; the dashboard
  * reads `.gitnexus/shadow-parity/latest.json` and renders.
  *
+ * Related types — `ShadowAgreement`, `ShadowCallsite`, `ShadowDiff` — are
+ * defined alongside `diffResolutions` in `./diff.ts` and re-exported
+ * through the top-level `gitnexus-shared` barrel. Consumers import all
+ * three from `gitnexus-shared`, not from this module.
+ *
  * Part of RFC #909 Ring 2 SHARED — #918.
  */
 // ─── Public API ─────────────────────────────────────────────────────────────

package/dist/_shared/scope-resolution/shadow/aggregate.js.map

@@ -1 +1 @@
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+{"version":3,"file":"aggregate.js","sourceRoot":"","sources":["../../../src/scope-resolution/shadow/aggregate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAwCH,+EAA+E;AAE/E;;;;;;;;;;GAUG;AACH,MAAM,UAAU,cAAc,CAC5B,KAAsF,EACtF,MAAY,IAAI,IAAI,EAAE;IAEtB,MAAM,cAAc,GAAG,IAAI,GAAG,EAAqC,CAAC;IAEpE,KAAK,MAAM,EAAE,QAAQ,EAAE,IAAI,EAAE,IAAI,KAAK,EAAE,CAAC;QACvC,IAAI,MAAM,GAAG,cAAc,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC1C,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,GAAG,eAAe,EAAE,CAAC;YAC3B,cAAc,CAAC,GAAG,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;QACvC,CAAC;QACD,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;IAC1B,CAAC;IAED,MAAM,WAAW,GAAwB,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,OAAO,EAAE,CAAC;SAC1E,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;SACvD,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC;IAExD,MAAM,OAAO,GAAG,eAAe,CAAC,WAAW,CAAC,CAAC;IAE7C,OAAO;QACL,WAAW,EAAE,GAAG,CAAC,WAAW,EAAE;QAC9B,WAAW;QACX,OAAO;KACR,CAAC;AACJ,CAAC;AAcD,SAAS,eAAe;IACtB,OAAO;QACL,UAAU,EAAE,CAAC;QACb,SAAS,EAAE,CAAC;QACZ,UAAU,EAAE,CAAC;QACb,OAAO,EAAE,CAAC;QACV,YAAY,EAAE,CAAC;QACf,SAAS,EAAE,CAAC;QACZ,iBAAiB,EAAE,IAAI,GAAG,EAAE;KAC7B,CAAC;AACJ,CAAC;AAED,SAAS,SAAS,CAAC,MAAqB,EAAE,IAAgB;IACxD,MAAM,CAAC,UAAU,IAAI,CAAC,CAAC;IACvB,kBAAkB,CAAC,MAAM,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC;IAC3C,IAAI,IAAI,CAAC,SAAS,KAAK,YAAY,IAAI,IAAI,CAAC,SAAS,KAAK,YAAY;QAAE,OAAO;IAC/E,KAAK,MAAM,EAAE,IAAI,IAAI,CAAC,aAAa,EAAE,CAAC;QACpC,MAAM,CAAC,iBAAiB,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,iBAAiB,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;IAC1F,CAAC;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,MAAqB,EAAE,SAA0B;IAC3E,QAAQ,SAAS,EAAE,CAAC;QAClB,KAAK,YAAY;YACf,MAAM,CAAC,SAAS,IAAI,CAAC,CAAC;YACtB,OAAO;QACT,KAAK,aAAa;YAChB,MAAM,CAAC,UAAU,IAAI,CAAC,CAAC;YACvB,OAAO;QACT,KAAK,UAAU;YACb,MAAM,CAAC,OAAO,IAAI,CAAC,CAAC;YACpB,OAAO;QACT,KAAK,eAAe;YAClB,MAAM,CAAC,YAAY,IAAI,CAAC,CAAC;YACzB,OAAO;QACT,KAAK,YAAY;YACf,MAAM,CAAC,SAAS,IAAI,CAAC,CAAC;YACtB,OAAO;IACX,CAAC;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,QAA4B,EAAE,MAAqB;IACnE,MAAM,QAAQ,GAAG,MAAM,CAAC,UAAU,GAAG,MAAM,CAAC,SAAS,CAAC;IACtD,MAAM,MAAM,GAAG,QAAQ,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,SAAS,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC;IAC9D,OAAO;QACL,QAAQ;QACR,UAAU,EAAE,MAAM,CAAC,UAAU;QAC7B,SAAS,EAAE,MAAM,CAAC,SAAS;QAC3B,UAAU,EAAE,MAAM,CAAC,UAAU;QAC7B,OAAO,EAAE,MAAM,CAAC,OAAO;QACvB,YAAY,EAAE,MAAM,CAAC,YAAY;QACjC,SAAS,EAAE,MAAM,CAAC,SAAS;QAC3B,MAAM;QACN,qEAAqE;QACrE,gDAAgD;QAChD,iBAAiB,EAAE,IAAI,GAAG,CACxB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CACtF;KACF,CAAC;AACJ,CAAC;AAED,SAAS,eAAe,CACtB,WAAyC;IAEzC,IAAI,UAAU,GAAG,CAAC,CAAC;IACnB,IAAI,SAAS,GAAG,CAAC,CAAC;IAClB,IAAI,UAAU,GAAG,CAAC,CAAC;IACnB,IAAI,OAAO,GAAG,CAAC,CAAC;IAChB,IAAI,YAAY,GAAG,CAAC,CAAC;IACrB,IAAI,SAAS,GAAG,CAAC,CAAC;IAClB,KAAK,MAAM,GAAG,IAAI,WAAW,EAAE,CAAC;QAC9B,UAAU,IAAI,GAAG,CAAC,UAAU,CAAC;QAC7B,SAAS,IAAI,GAAG,CAAC,SAAS,CAAC;QAC3B,UAAU,IAAI,GAAG,CAAC,UAAU,CAAC;QAC7B,OAAO,IAAI,GAAG,CAAC,OAAO,CAAC;QACvB,YAAY,IAAI,GAAG,CAAC,YAAY,CAAC;QACjC,SAAS,IAAI,GAAG,CAAC,SAAS,CAAC;IAC7B,CAAC;IACD,MAAM,QAAQ,GAAG,UAAU,GAAG,SAAS,CAAC;IACxC,MAAM,MAAM,GAAG,QAAQ,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC;IACvD,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,UAAU,EAAE,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,MAAM,EAAE,CAAC;AACzF,CAAC"}

package/dist/_shared/scope-resolution/types.d.ts

@@ -182,6 +182,17 @@ export interface ParsedTypeBinding {
  * concretely typed in Ring 2 SHARED (#915).
  */
 export type WorkspaceIndex = unknown;
+/**
+ * Minimal scope-lookup contract: map a `ScopeId` back to its `Scope` record.
+ *
+ * Lives in the data-model layer so both `ScopeTree` (§3.1) and
+ * `resolveTypeRef` / `Registry.lookup` (§4) can depend on it without
+ * inverting each other. `ScopeTree` is the canonical implementation;
+ * tests and future alternative containers may supply their own.
+ */
+export interface ScopeLookup {
+    getScope(id: ScopeId): Scope | undefined;
+}
 /** Call-site description passed to `arityCompatibility`. */
 export interface Callsite {
     /** Number of arguments at the call site. */

package/dist/_shared/scope-resolution/types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../src/scope-resolution/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AACnD,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAI/D,4FAA4F;AAC5F,MAAM,MAAM,OAAO,GAAG,MAAM,CAAC;AAE7B,0DAA0D;AAC1D,MAAM,MAAM,KAAK,GAAG,MAAM,CAAC;AAE3B,2DAA2D;AAC3D,MAAM,MAAM,SAAS,GACjB,QAAQ,GACR,WAAW,GACX,OAAO,GACP,UAAU,GACV,OAAO,GACP,YAAY,CAAC;AAIjB,qFAAqF;AACrF,MAAM,WAAW,KAAK;IACpB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;CACzB;AAED;;;;;;GAMG;AACH,MAAM,WAAW,OAAO;IACtB,6FAA6F;IAC7F,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,KAAK,EAAE,KAAK,CAAC;IACtB,gCAAgC;IAChC,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;CACvB;AAED;;;;;GAKG;AACH,MAAM,MAAM,YAAY,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;AAI7D;;;;;;;;;;;;;GAaG;AACH,MAAM,MAAM,YAAY;AACtB;;;;;;;GAOG;AACD;IACE,QAAQ,CAAC,IAAI,EAAE,OAAO,CAAC;IACvB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;CAC5B;AACH;;;;;;GAMG;GACD;IACE,QAAQ,CAAC,IAAI,EAAE,OAAO,CAAC;IACvB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;CAC5B;AACH;;;;;;;;;;GAUG;GACD;IACE,QAAQ,CAAC,IAAI,EAAE,WAAW,CAAC;IAC3B,wFAAwF;IACxF,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,mEAAmE;IACnE,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;CAC5B;AACH;;;;;;;;;;GAUG;GACD;IACE,QAAQ,CAAC,IAAI,EAAE,UAAU,CAAC;IAC1B,iDAAiD;IACjD,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,iCAAiC;IACjC,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,uFAAuF;IACvF,QAAQ,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC;CACzB;AACH;;;;;;;;;;GAUG;GACD;IACE,QAAQ,CAAC,IAAI,EAAE,UAAU,CAAC;IAC1B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;CAC5B;AACH;;;;;;;;;GASG;GACD;IACE,QAAQ,CAAC,IAAI,EAAE,oBAAoB,CAAC;IACpC,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,iFAAiF;IACjF,QAAQ,CAAC,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;CACnC,CAAC;AAEN;;;;;GAKG;AACH,MAAM,WAAW,iBAAiB;IAChC,wEAAwE;IACxE,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,6EAA6E;IAC7E,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,QAAQ,CAAC,MAAM,EAAE,OAAO,CAAC,QAAQ,CAAC,CAAC;CACpC;AAED;;;;GAIG;AACH,MAAM,MAAM,cAAc,GAAG,OAAO,CAAC;AAMrC;;;;;;;GAOG;AACH,MAAM,WAAW,WAAW;IAC1B,QAAQ,CAAC,EAAE,EAAE,OAAO,GAAG,KAAK,GAAG,SAAS,CAAC;CAC1C;AAED,4DAA4D;AAC5D,MAAM,WAAW,QAAQ;IACvB,4CAA4C;IAC5C,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;CACxB;AAID;;;;;;GAMG;AACH,MAAM,WAAW,UAAU;IACzB,2DAA2D;IAC3D,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,wEAAwE;IACxE,QAAQ,CAAC,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;IACnC,2DAA2D;IAC3D,QAAQ,CAAC,kBAAkB,EAAE,MAAM,CAAC;IACpC,wEAAwE;IACxE,QAAQ,CAAC,iBAAiB,CAAC,EAAE,OAAO,CAAC;IACrC,+DAA+D;IAC/D,QAAQ,CAAC,WAAW,CAAC,EAAE,KAAK,CAAC;IAC7B,QAAQ,CAAC,IAAI,EACT,OAAO,GACP,OAAO,GACP,WAAW,GACX,mBAAmB,GACnB,UAAU,GACV,oBAAoB,CAAC;IACzB,oFAAoF;IACpF,QAAQ,CAAC,aAAa,CAAC,EAAE,SAAS,MAAM,EAAE,CAAC;IAC3C,4EAA4E;IAC5E,QAAQ,CAAC,UAAU,CAAC,EAAE,YAAY,CAAC;CACpC;AAID;;;;;;;GAOG;AACH,MAAM,WAAW,UAAU;IACzB,QAAQ,CAAC,GAAG,EAAE,gBAAgB,CAAC;IAC/B,QAAQ,CAAC,MAAM,EAAE,OAAO,GAAG,QAAQ,GAAG,WAAW,GAAG,UAAU,GAAG,UAAU,CAAC;IAC5E,sGAAsG;IACtG,QAAQ,CAAC,GAAG,CAAC,EAAE,UAAU,CAAC;CAC3B;AAID;;;;;;;;GAQG;AACH,MAAM,WAAW,OAAO;IACtB,iFAAiF;IACjF,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,6FAA6F;IAC7F,QAAQ,CAAC,eAAe,EAAE,OAAO,CAAC;IAClC,QAAQ,CAAC,MAAM,EACX,YAAY,GACZ,sBAAsB,GACtB,mBAAmB,GACnB,MAAM,GACN,qBAAqB,GACrB,sBAAsB,GACtB,qBAAqB,CAAC;IAC1B,iGAAiG;IACjG,QAAQ,CAAC,QAAQ,CAAC,EAAE,SAAS,OAAO,EAAE,CAAC;CACxC;AAID;;;;;GAKG;AACH,MAAM,WAAW,KAAK;IACpB,QAAQ,CAAC,EAAE,EAAE,OAAO,CAAC;IACrB,QAAQ,CAAC,MAAM,EAAE,OAAO,GAAG,IAAI,CAAC;IAChC,QAAQ,CAAC,IAAI,EAAE,SAAS,CAAC;IACzB,QAAQ,CAAC,KAAK,EAAE,KAAK,CAAC;IACtB,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAE1B,mFAAmF;IACnF,QAAQ,CAAC,QAAQ,EAAE,WAAW,CAAC,MAAM,EAAE,SAAS,UAAU,EAAE,CAAC,CAAC;IAE9D,yFAAyF;IACzF,QAAQ,CAAC,SAAS,EAAE,SAAS,gBAAgB,EAAE,CAAC;IAEhD;;kDAE8C;IAC9C,QAAQ,CAAC,OAAO,EAAE,SAAS,UAAU,EAAE,CAAC;IAExC,8FAA8F;IAC9F,QAAQ,CAAC,YAAY,EAAE,WAAW,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CACrD;AAID;;;;;GAKG;AACH,MAAM,WAAW,kBAAkB;IACjC,QAAQ,CAAC,IAAI,EACT,OAAO,GACP,aAAa,GACb,QAAQ,GACR,cAAc,GACd,aAAa,GACb,YAAY,GACZ,aAAa,GACb,aAAa,GACb,kBAAkB,GAClB,2BAA2B,CAAC;IAChC,kFAAkF;IAClF,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;IACxB,oEAAoE;IACpE,QAAQ,CAAC,IAAI,CAAC,EAAE,MAAM,CAAC;CACxB;AAED;;;;;GAKG;AACH,MAAM,WAAW,UAAU;IACzB,QAAQ,CAAC,GAAG,EAAE,gBAAgB,CAAC;IAC/B,+CAA+C;IAC/C,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,QAAQ,CAAC,QAAQ,EAAE,SAAS,kBAAkB,EAAE,CAAC;IACjD,0DAA0D;IAC1D,QAAQ,CAAC,IAAI,CAAC,EAAE,SAAS,OAAO,EAAE,CAAC;CACpC;AAID;;;;;GAKG;AACH,MAAM,WAAW,SAAS;IACxB,oDAAoD;IACpD,QAAQ,CAAC,SAAS,EAAE,OAAO,CAAC;IAC5B,QAAQ,CAAC,KAAK,EAAE,KAAK,CAAC;IACtB,2CAA2C;IAC3C,QAAQ,CAAC,OAAO,EAAE,KAAK,CAAC;IACxB,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,OAAO,GAAG,gBAAgB,GAAG,UAAU,GAAG,YAAY,CAAC;IACxF,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,QAAQ,CAAC,QAAQ,EAAE,SAAS,kBAAkB,EAAE,CAAC;CAClD;AAED;;;GAGG;AACH,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,aAAa,EAAE,WAAW,CAAC,OAAO,EAAE,SAAS,SAAS,EAAE,CAAC,CAAC;IACnE,QAAQ,CAAC,WAAW,EAAE,WAAW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package/dist/cli/ai-context.js

@@ -13,6 +13,32 @@ const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
 const GITNEXUS_START_MARKER = '<!-- gitnexus:start -->';
 const GITNEXUS_END_MARKER = '<!-- gitnexus:end -->';
+/**
+ * Find the index of a section marker that occupies its own line.
+ * Unlike `indexOf`, this rejects inline prose references like
+ * `` See the `<!-- gitnexus:start -->` block `` that appear
+ * mid-sentence (#1041). A marker counts as section-position only when:
+ *   - preceded by newline or start-of-file, AND
+ *   - followed by newline, `\r` (CRLF files), or end-of-file.
+ * The generator always emits each marker alone on its line, so this
+ * matches every legitimate section and none of the inline mentions.
+ *
+ * `startFrom` lets the end-marker lookup start after the already-found
+ * start marker, avoiding a scan from 0 and guaranteeing we never pick
+ * up an end marker that appears earlier in the file than the start.
+ */
+function findSectionMarkerIndex(content, marker, startFrom = 0) {
+    let idx = content.indexOf(marker, startFrom);
+    while (idx !== -1) {
+        const atLineStart = idx === 0 || content[idx - 1] === '\n';
+        const endPos = idx + marker.length;
+        const atLineEnd = endPos === content.length || content[endPos] === '\n' || content[endPos] === '\r';
+        if (atLineStart && atLineEnd)
+            return idx;
+        idx = content.indexOf(marker, idx + 1);
+    }
+    return -1;
+}
 /**
  * Generate the full GitNexus context content.
  *
@@ -89,7 +115,7 @@ This project is indexed by GitNexus as **${projectName}**${noStats ? '' : ` (${s
 ${groupNames && groupNames.length > 0
         ? `## Cross-Repo Groups
 
-This repository is listed under GitNexus **group(s): ${groupNames.join(', ')}** (see \`~/.gitnexus/groups/\`). For blast radius across repository boundaries, use MCP tools \`group_impact\`, \`group_sync\`, \`group_query\`, \`group_contracts\`, \`group_status\`, and \`group_list\`. From the terminal: \`npx gitnexus group list\`, \`npx gitnexus group sync <name>\`, \`npx gitnexus group impact <name> --target <symbol> --repo <group-path>\`.
+This repository is listed under GitNexus **group(s): ${groupNames.join(', ')}** (see \`~/.gitnexus/groups/\`). For cross-repo analysis, use MCP tools \`impact\`, \`query\`, and \`context\` with \`repo\` set to \`@<groupName>\` or \`@<groupName>/<memberPath>\` (paths match keys in that group’s \`group.yaml\`). Use \`group_list\` / \`group_sync\` for membership and sync. From the terminal: \`npx gitnexus group list\`, \`npx gitnexus group sync <name>\`, \`npx gitnexus group impact <name> --target <symbol> --repo <group-path>\`.
 
 `
         : ''}## CLI
@@ -123,9 +149,14 @@ async function upsertGitNexusSection(filePath, content) {
         return 'created';
     }
     const existingContent = await fs.readFile(filePath, 'utf-8');
-    // Check if GitNexus section already exists
-    const startIdx = existingContent.indexOf(GITNEXUS_START_MARKER);
-    const endIdx = existingContent.indexOf(GITNEXUS_END_MARKER);
+    // Check if GitNexus section already exists. Matching is restricted
+    // to markers that occupy their own line so that inline prose
+    // references (e.g. `` See the `<!-- gitnexus:start -->` block `` in
+    // the shipped CLAUDE.md) are NOT treated as section delimiters
+    // (#1041). The end-marker scan starts after the start-marker so it
+    // can never pick up an earlier end in the file.
+    const startIdx = findSectionMarkerIndex(existingContent, GITNEXUS_START_MARKER);
+    const endIdx = findSectionMarkerIndex(existingContent, GITNEXUS_END_MARKER, startIdx === -1 ? 0 : startIdx);
     if (startIdx !== -1 && endIdx !== -1 && endIdx > startIdx) {
         // Replace existing section
         const before = existingContent.substring(0, startIdx);

package/dist/cli/analyze.d.ts

@@ -10,6 +10,12 @@
 export interface AnalyzeOptions {
     force?: boolean;
     embeddings?: boolean;
+    /**
+     * Explicitly drop existing embeddings on rebuild instead of preserving
+     * them. Without this flag, a routine `analyze` keeps any embeddings
+     * already present in the index even when `--embeddings` is omitted.
+     */
+    dropEmbeddings?: boolean;
     skills?: boolean;
     verbose?: boolean;
     /** Skip AGENTS.md and CLAUDE.md gitnexus block updates. */
@@ -18,5 +24,26 @@ export interface AnalyzeOptions {
     noStats?: boolean;
     /** Index the folder even when no .git directory is present. */
     skipGit?: boolean;
+    /**
+     * Override the default basename-derived registry `name` with a
+     * user-supplied alias (#829). Disambiguates repos whose paths share a
+     * basename. Persisted — subsequent re-analyses of the same path without
+     * `--name` preserve the alias.
+     */
+    name?: string;
+    /**
+     * Allow registration even when another path already uses the same
+     * `--name` alias (#829). Intentionally a distinct flag from `--force`
+     * because the user may want to coexist under the same name WITHOUT
+     * paying the cost of a pipeline re-index. Maps to registerRepo's
+     * `allowDuplicateName` option end-to-end.
+     */
+    allowDuplicateName?: boolean;
+    /**
+     * Override the walker's large-file skip threshold (#991). Value in KB;
+     * clamped downstream to the tree-sitter 32 MB ceiling. Sets
+     * `GITNEXUS_MAX_FILE_SIZE` for the rest of the pipeline.
+     */
+    maxFileSize?: string;
 }
 export declare const analyzeCommand: (inputPath?: string, options?: AnalyzeOptions) => Promise<void>;

package/dist/cli/analyze.js

@@ -12,9 +12,10 @@ import { execFileSync } from 'child_process';
 import v8 from 'v8';
 import cliProgress from 'cli-progress';
 import { closeLbug } from '../core/lbug/lbug-adapter.js';
-import { getStoragePaths, getGlobalRegistryPath } from '../storage/repo-manager.js';
+import { getStoragePaths, getGlobalRegistryPath, RegistryNameCollisionError, } from '../storage/repo-manager.js';
 import { getGitRoot, hasGitDir } from '../storage/git.js';
 import { runFullAnalysis } from '../core/run-analyze.js';
+import { getMaxFileSizeBannerMessage } from '../core/ingestion/utils/max-file-size.js';
 import fs from 'fs/promises';
 const HEAP_MB = 8192;
 const HEAP_FLAG = `--max-old-space-size=${HEAP_MB}`;
@@ -51,6 +52,9 @@ export const analyzeCommand = async (inputPath, options) => {
     if (options?.verbose) {
         process.env.GITNEXUS_VERBOSE = '1';
     }
+    if (options?.maxFileSize) {
+        process.env.GITNEXUS_MAX_FILE_SIZE = options.maxFileSize;
+    }
     console.log('\n  GitNexus Analyzer\n');
     let repoPath;
     if (inputPath) {
@@ -85,6 +89,10 @@ export const analyzeCommand = async (inputPath, options) => {
     if (process.env.GITNEXUS_NO_GITIGNORE) {
         console.log('  GITNEXUS_NO_GITIGNORE is set — skipping .gitignore (still reading .gitnexusignore)\n');
     }
+    const maxFileSizeBanner = getMaxFileSizeBannerMessage();
+    if (maxFileSizeBanner) {
+        console.log(`${maxFileSizeBanner}\n`);
+    }
     // ── CLI progress bar setup ─────────────────────────────────────────
     const bar = new cliProgress.SingleBar({
         format: '  {bar} {percentage}% | {phase}',
@@ -146,11 +154,21 @@ export const analyzeCommand = async (inputPath, options) => {
     // ── Run shared analysis orchestrator ───────────────────────────────
     try {
         const result = await runFullAnalysis(repoPath, {
+            // Pipeline re-index — OR'd with --skills because skill generation
+            // needs a fresh pipelineResult. Has no bearing on the registry
+            // collision guard (see allowDuplicateName below).
             force: options?.force || options?.skills,
             embeddings: options?.embeddings,
+            dropEmbeddings: options?.dropEmbeddings,
             skipGit: options?.skipGit,
             skipAgentsMd: options?.skipAgentsMd,
             noStats: options?.noStats,
+            registryName: options?.name,
+            // Registry-collision bypass — its own CLI flag, intentionally NOT
+            // overloading --force. A user who hits the collision guard should
+            // be able to accept the duplicate name without also paying the
+            // cost of a full pipeline re-index. See #829 review round 2.
+            allowDuplicateName: options?.allowDuplicateName,
         }, {
             onProgress: (_phase, percent, message) => {
                 updateBar(percent, message);
@@ -234,6 +252,18 @@ export const analyzeCommand = async (inputPath, options) => {
         console.error = origError;
         bar.stop();
         const msg = err.message || String(err);
+        // Registry name-collision from --name (#829) — surface as an
+        // actionable error rather than a generic stack-trace.
+        if (err instanceof RegistryNameCollisionError) {
+            console.error(`\n  Registry name collision:\n`);
+            console.error(`    "${err.registryName}" is already used by "${err.existingPath}".\n`);
+            console.error(`  Options:`);
+            console.error(`    • Pick a different alias:  gitnexus analyze --name <alias>`);
+            console.error(`    • Allow the duplicate:     gitnexus analyze --allow-duplicate-name  (leaves "-r ${err.registryName}" ambiguous)`);
+            console.error('');
+            process.exitCode = 1;
+            return;
+        }
         console.error(`\n  Analysis failed: ${msg}\n`);
         // Provide helpful guidance for known failure modes
         if (msg.includes('Maximum call stack size exceeded') ||

package/dist/cli/clean.js

@@ -5,7 +5,7 @@
  * Also unregisters it from the global registry.
  */
 import fs from 'fs/promises';
-import { findRepo, unregisterRepo, listRegisteredRepos } from '../storage/repo-manager.js';
+import { findRepo, unregisterRepo, listRegisteredRepos, assertSafeStoragePath, UnsafeStoragePathError, } from '../storage/repo-manager.js';
 export const cleanCommand = async (options) => {
     // --all flag: clean all indexed repos
     if (options?.all) {
@@ -24,6 +24,24 @@ export const cleanCommand = async (options) => {
         }
         const entries = await listRegisteredRepos();
         for (const entry of entries) {
+            // Safety guard (#1003 review — @magyargergo): same rationale as
+            // remove.ts. `~/.gitnexus/registry.json` is user-writable, so a
+            // corrupted or hand-edited entry could point storagePath at the
+            // repo root, an empty string, or anywhere else — and
+            // fs.rm(recursive: true) on any of those would be catastrophic.
+            // Skip poisoned entries without touching disk, but keep going
+            // through the rest of the registry (preserves the existing
+            // per-repo error-tolerance semantics of `clean --all`).
+            try {
+                assertSafeStoragePath(entry);
+            }
+            catch (err) {
+                if (err instanceof UnsafeStoragePathError) {
+                    console.error(`Refusing to clean ${entry.name}: ${err.message}`);
+                    continue;
+                }
+                throw err;
+            }
             try {
                 await fs.rm(entry.storagePath, { recursive: true, force: true });
                 await unregisterRepo(entry.path);

package/dist/cli/group.js

@@ -149,6 +149,79 @@ export function registerGroupCommands(program) {
             console.log(`\nWrote contracts.json (${result.contracts.length} contracts, ${result.crossLinks.length} cross-links)`);
         }
     });
+    group
+        .command('impact <name>')
+        .description('Cross-repo impact for a symbol in one member repo of a group')
+        .requiredOption('--target <symbol>', 'Symbol or file name to analyze')
+        .requiredOption('--repo <groupPath>', 'Member path from group.yaml (e.g. app/backend), not the indexed repo name')
+        .option('--direction <dir>', 'upstream or downstream', 'upstream')
+        .option('--service <path>', 'Optional monorepo service directory prefix (path filter)')
+        .option('--subgroup <path>', 'Optional prefix limiting which group repos participate in cross fan-out')
+        .option('--max-depth <n>', 'Max graph traversal depth')
+        .option('--cross-depth <n>', 'Cross-repository hop depth')
+        .option('--min-confidence <n>', 'Minimum relation confidence (0–1)')
+        .option('--include-tests', 'Include test files in traversal', false)
+        .option('--timeout-ms <n>', 'Phase-1 local impact wall time in milliseconds')
+        .option('--json', 'JSON output')
+        .action(async (name, opts) => {
+        const { LocalBackend } = await import('../mcp/local/local-backend.js');
+        const backend = new LocalBackend();
+        try {
+            await backend.init();
+            const payload = {
+                name,
+                repo: opts.repo,
+                target: opts.target,
+                direction: opts.direction || 'upstream',
+            };
+            if (opts.service)
+                payload.service = opts.service;
+            if (opts.subgroup)
+                payload.subgroup = opts.subgroup;
+            if (opts.maxDepth !== undefined && opts.maxDepth !== '') {
+                const n = parseInt(String(opts.maxDepth), 10);
+                if (!Number.isNaN(n))
+                    payload.maxDepth = n;
+            }
+            if (opts.crossDepth !== undefined && opts.crossDepth !== '') {
+                const n = parseInt(String(opts.crossDepth), 10);
+                if (!Number.isNaN(n))
+                    payload.crossDepth = n;
+            }
+            if (opts.minConfidence !== undefined && opts.minConfidence !== '') {
+                const n = parseFloat(String(opts.minConfidence));
+                if (!Number.isNaN(n))
+                    payload.minConfidence = n;
+            }
+            if (opts.timeoutMs !== undefined && opts.timeoutMs !== '') {
+                const n = parseInt(String(opts.timeoutMs), 10);
+                if (!Number.isNaN(n))
+                    payload.timeoutMs = n;
+            }
+            if (opts.includeTests)
+                payload.includeTests = true;
+            const raw = await backend.getGroupService().groupImpact(payload);
+            if (raw && typeof raw === 'object' && 'error' in raw) {
+                console.error(String(raw.error));
+                process.exitCode = 1;
+                return;
+            }
+            if (opts.json) {
+                console.log(JSON.stringify(raw, null, 2));
+            }
+            else {
+                const summary = raw?.summary;
+                const risk = raw?.risk;
+                console.log(`Group impact for "${name}" (${String(opts.repo)}): risk=${risk ?? '?'}`);
+                if (summary) {
+                    console.log(`  direct=${summary.direct ?? 0} processes=${summary.processes_affected ?? 0} cross=${summary.cross_repo_hits ?? 0}`);
+                }
+            }
+        }
+        finally {
+            await backend.dispose().catch(() => { });
+        }
+    });
     group
         .command('query <name> <query>')
         .description('Search execution flows across all repos in a group')

package/dist/cli/index-repo.js

@@ -11,7 +11,7 @@
 import path from 'path';
 import fs from 'fs/promises';
 import { getStoragePaths, loadMeta, addToGitignore, registerRepo, } from '../storage/repo-manager.js';
-import { getGitRoot, isGitRepo } from '../storage/git.js';
+import { getGitRoot, getRemoteUrl, isGitRepo } from '../storage/git.js';
 export const indexCommand = async (inputPathParts, options) => {
     console.log('\n  GitNexus Index\n');
     const inputPath = inputPathParts?.length ? inputPathParts.join(' ') : undefined;
@@ -88,6 +88,13 @@ export const indexCommand = async (inputPathParts, options) => {
         };
     }
     // ── Register in global registry ───────────────────────────────────
+    // Refresh the on-disk meta with a freshly captured `remoteUrl` if
+    // it's missing, so an `index` of an older `.gitnexus/` still gets
+    // sibling-clone fingerprinting on subsequent use without forcing a
+    // full re-analyze.
+    if (!meta.remoteUrl && isGitRepo(repoPath)) {
+        meta.remoteUrl = getRemoteUrl(repoPath);
+    }
     await registerRepo(repoPath, meta);
     await addToGitignore(repoPath);
     const projectName = path.basename(repoPath);

package/dist/cli/index.js

@@ -18,12 +18,23 @@ program
     .description('Index a repository (full analysis)')
     .option('-f, --force', 'Force full re-index even if up to date')
     .option('--embeddings', 'Enable embedding generation for semantic search (off by default)')
+    .option('--drop-embeddings', 'Drop existing embeddings on rebuild. By default, an `analyze` without `--embeddings` ' +
+    'preserves any embeddings already present in the index.')
     .option('--skills', 'Generate repo-specific skill files from detected communities')
     .option('--skip-agents-md', 'Skip updating the gitnexus section in AGENTS.md and CLAUDE.md')
     .option('--no-stats', 'Omit volatile file/symbol counts from AGENTS.md and CLAUDE.md')
     .option('--skip-git', 'Index a folder without requiring a .git directory')
+    .option('--name <alias>', 'Register this repo under a custom name in ~/.gitnexus/registry.json ' +
+    '(disambiguates repos whose paths share a basename, e.g. two different .../app folders)')
+    .option('--allow-duplicate-name', 'Register this repo even if another path already uses the same --name alias. ' +
+    'Leaves `-r <name>` ambiguous for the two paths; use -r <path> to disambiguate.')
     .option('-v, --verbose', 'Enable verbose ingestion warnings (default: false)')
-    .addHelpText('after', '\nEnvironment variables:\n  GITNEXUS_NO_GITIGNORE=1  Skip .gitignore parsing (still reads .gitnexusignore)')
+    .option('--max-file-size <kb>', 'Skip files larger than this (KB). Default: 512. Hard cap: 32768 (tree-sitter limit).')
+    .addHelpText('after', '\nEnvironment variables:\n' +
+    '  GITNEXUS_NO_GITIGNORE=1   Skip .gitignore parsing (still reads .gitnexusignore)\n' +
+    '  GITNEXUS_MAX_FILE_SIZE=N  Override large-file skip threshold (KB). Default 512, max 32768.\n' +
+    '\nTip: `.gitnexusignore` supports `.gitignore`-style negation. Add e.g.\n' +
+    '     `!__tests__/` to index a directory that is auto-filtered by default (#771).')
     .action(createLazyAction(() => import('./analyze.js'), 'analyzeCommand'));
 program
     .command('index [path...]')
@@ -55,6 +66,12 @@ program
     .option('-f, --force', 'Skip confirmation prompt')
     .option('--all', 'Clean all indexed repos')
     .action(createLazyAction(() => import('./clean.js'), 'cleanCommand'));
+program
+    .command('remove <target>')
+    .description('Delete the GitNexus index for a registered repo (by alias, name, or absolute path). ' +
+    'Unlike `clean`, does not require being inside the repo. Idempotent on unknown targets.')
+    .option('-f, --force', 'Skip confirmation prompt')
+    .action(createLazyAction(() => import('./remove.js'), 'removeCommand'));
 program
     .command('wiki [path]')
     .description('Generate repository wiki from knowledge graph')
@@ -107,6 +124,14 @@ program
     .description('Execute raw Cypher query against the knowledge graph')
     .option('-r, --repo <name>', 'Target repository')
     .action(createLazyAction(() => import('./tool.js'), 'cypherCommand'));
+program
+    .command('detect-changes')
+    .alias('detect_changes')
+    .description('Map git diff hunks to indexed symbols and affected execution flows')
+    .option('-s, --scope <scope>', 'What to analyze: unstaged, staged, all, or compare', 'unstaged')
+    .option('-b, --base-ref <ref>', 'Branch/commit for compare scope (e.g. main)')
+    .option('-r, --repo <name>', 'Target repository')
+    .action(createLazyAction(() => import('./tool.js'), 'detectChangesCommand'));
 // ─── Eval Server (persistent daemon for SWE-bench) ─────────────────
 program
     .command('eval-server')