npm - gitnexus - Versions diffs - 1.6.3-rc.9 → 1.6.3 - Mend

gitnexus 1.6.3-rc.9 → 1.6.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (257) hide show

package/dist/_shared/scope-resolution/registries/evidence.js CHANGED Viewed

@@ -124,6 +124,11 @@ function getOriginWeight(origin) {
         case 'global-qualified':
             return EvidenceWeights.globalQualified;
         case 'global-name':
+            // Reserved for Ring 3 byName global index. `lookupCore` today only
+            // emits `'global-qualified'` (via `lookupQualified`, dotted-name
+            // fallback); no code path constructs `origin: 'global-name'` yet.
+            // Kept here so the Appendix A weight stays live and `composeEvidence`
+            // remains exhaustive over the origin union.
             return EvidenceWeights.globalName;
     }
 }

package/dist/_shared/scope-resolution/registries/evidence.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"evidence.js","sourceRoot":"","sources":["../../../src/scope-resolution/registries/evidence.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAGH,OAAO,EAAE,eAAe,EAAE,wBAAwB,EAAE,MAAM,wBAAwB,CAAC;AAkCnF;;;;;;;GAOG;AACH,MAAM,UAAU,eAAe,CAAC,OAAmB;IACjD,MAAM,GAAG,GAAyB,EAAE,CAAC;IAErC,0EAA0E;IAC1E,IAAI,OAAO,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;QACjC,MAAM,UAAU,GAAG,eAAe,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QACnD,MAAM,MAAM,GAAG,OAAO,CAAC,iBAAiB;YACtC,CAAC,CAAC,UAAU,GAAG,eAAe,CAAC,wBAAwB;YACvD,CAAC,CAAC,UAAU,CAAC;QACf,MAAM,YAAY,GAAG,sBAAsB,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QAC5D,GAAG,CAAC,IAAI,CAAC;YACP,IAAI,EAAE,YAAY;YAClB,MAAM,EAAE,MAAM;YACd,GAAG,CAAC,OAAO,CAAC,iBAAiB;gBAC3B,CAAC,CAAC,EAAE,IAAI,EAAE,0BAA0B,eAAe,CAAC,wBAAwB,QAAQ,EAAE;gBACtF,CAAC,CAAC,EAAE,CAAC;SACR,CAAC,CAAC;IACL,CAAC;IAED,uEAAuE;IACvE,uEAAuE;IACvE,sEAAsE;IACtE,IAAI,OAAO,CAAC,eAAe,KAAK,SAAS,IAAI,OAAO,CAAC,eAAe,GAAG,CAAC,EAAE,CAAC;QACzE,GAAG,CAAC,IAAI,CAAC;YACP,IAAI,EAAE,aAAa;YACnB,MAAM,EAAE,eAAe,CAAC,kBAAkB,GAAG,OAAO,CAAC,eAAe;YACpE,IAAI,EAAE,SAAS,OAAO,CAAC,eAAe,EAAE;SACzC,CAAC,CAAC;IACL,CAAC;IAED,0EAA0E;IAC1E,IAAI,OAAO,CAAC,mBAAmB,KAAK,SAAS,EAAE,CAAC;QAC9C,GAAG,CAAC,IAAI,CAAC;YACP,IAAI,EAAE,cAAc;YACpB,MAAM,EAAE,wBAAwB,CAAC,OAAO,CAAC,mBAAmB,CAAC;YAC7D,IAAI,EAAE,YAAY,OAAO,CAAC,mBAAmB,EAAE;SAChD,CAAC,CAAC;IACL,CAAC;IAED,0EAA0E;IAC1E,IAAI,OAAO,CAAC,UAAU,KAAK,IAAI,EAAE,CAAC;QAChC,GAAG,CAAC,IAAI,CAAC;YACP,IAAI,EAAE,aAAa;YACnB,MAAM,EAAE,eAAe,CAAC,UAAU;SACnC,CAAC,CAAC;IACL,CAAC;IAED,0EAA0E;IAC1E,GAAG,CAAC,IAAI,CAAC;QACP,IAAI,EAAE,YAAY;QAClB,MAAM,EAAE,eAAe,CAAC,SAAS;KAClC,CAAC,CAAC;IAEH,0EAA0E;IAC1E,IAAI,OAAO,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;QACvC,MAAM,MAAM,GACV,OAAO,CAAC,YAAY,KAAK,YAAY;YACnC,CAAC,CAAC,eAAe,CAAC,oBAAoB;YACtC,CAAC,CAAC,OAAO,CAAC,YAAY,KAAK,cAAc;gBACvC,CAAC,CAAC,eAAe,CAAC,sBAAsB;gBACxC,CAAC,CAAC,eAAe,CAAC,iBAAiB,CAAC;QAC1C,GAAG,CAAC,IAAI,CAAC;YACP,IAAI,EAAE,aAAa;YACnB,MAAM;YACN,IAAI,EAAE,OAAO,CAAC,YAAY;SAC3B,CAAC,CAAC;IACL,CAAC;IAED,0EAA0E;IAC1E,IAAI,OAAO,CAAC,iBAAiB,KAAK,IAAI,EAAE,CAAC;QACvC,GAAG,CAAC,IAAI,CAAC;YACP,IAAI,EAAE,2BAA2B;YACjC,MAAM,EAAE,eAAe,CAAC,uBAAuB;SAChD,CAAC,CAAC;IACL,CAAC;IAED,OAAO,GAAG,CAAC;AACb,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,sBAAsB,CAAC,QAAuC;IAC5E,IAAI,GAAG,GAAG,CAAC,CAAC;IACZ,KAAK,MAAM,CAAC,IAAI,QAAQ;QAAE,GAAG,IAAI,CAAC,CAAC,MAAM,CAAC;IAC1C,IAAI,GAAG,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IACtB,IAAI,GAAG,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IACtB,OAAO,GAAG,CAAC;AACb,CAAC;AAED,+EAA+E;AAE/E,SAAS,eAAe,CAAC,MAAyC;IAChE,QAAQ,MAAM,EAAE,CAAC;QACf,KAAK,OAAO;YACV,OAAO,eAAe,CAAC,KAAK,CAAC;QAC/B,KAAK,QAAQ;YACX,OAAO,eAAe,CAAC,MAAM,CAAC;QAChC,KAAK,UAAU;YACb,OAAO,eAAe,CAAC,QAAQ,CAAC;QAClC,KAAK,WAAW;YACd,OAAO,eAAe,CAAC,SAAS,CAAC;QACnC,KAAK,UAAU;YACb,OAAO,eAAe,CAAC,QAAQ,CAAC;QAClC,KAAK,kBAAkB;YACrB,OAAO,eAAe,CAAC,eAAe,CAAC;QACzC,KAAK,aAAa;YAChB,mEAAmE;YACnE,iEAAiE;YACjE,kEAAkE;YAClE,sEAAsE;YACtE,4CAA4C;YAC5C,OAAO,eAAe,CAAC,UAAU,CAAC;IACtC,CAAC;AACH,CAAC;AAED,SAAS,sBAAsB,CAC7B,MAAyC;IAEzC,QAAQ,MAAM,EAAE,CAAC;QACf,KAAK,OAAO;YACV,OAAO,OAAO,CAAC;QACjB,KAAK,QAAQ,CAAC;QACd,KAAK,UAAU,CAAC;QAChB,KAAK,WAAW,CAAC;QACjB,KAAK,UAAU;YACb,OAAO,QAAQ,CAAC;QAClB,KAAK,kBAAkB;YACrB,OAAO,kBAAkB,CAAC;QAC5B,KAAK,aAAa;YAChB,OAAO,aAAa,CAAC;IACzB,CAAC;AACH,CAAC"}

package/dist/_shared/scope-resolution/registries/lookup-core.js CHANGED Viewed

@@ -216,8 +216,9 @@ function lookupReceiverType(startScope, receiverName, ctx) {
             const candidateIds = ctx.qualifiedNames.get(typeRef.rawName);
             if (candidateIds.length === 1)
                 return candidateIds[0];
-            // If ambiguous or missing, try a name-match among class-like defs —
-            // but only when the rawName has no dots (simple name).
+            // Ambiguous (≥ 2) or missing (0) — caller must pre-resolve via
+            // `resolveTypeRef` (#916) if they want the richer semantics. We
+            // intentionally do NOT re-implement a simple-name fallback here.
             return undefined;
         }
         currentId = scope.parent;
@@ -247,15 +248,30 @@ function simpleNameOf(def) {
 }
 function recordTypeBindingHit(perCandidate, def, mroDepth, receiverOwner) {
     const state = ensureCandidate(perCandidate, def);
-    // Only replace if this hit is shallower (smaller MRO depth).
-    if (state.signals.typeBindingMroDepth === undefined ||
-        mroDepth < state.signals.typeBindingMroDepth) {
+    const existingMroDepth = state.signals.typeBindingMroDepth;
+    const firstHit = existingMroDepth === undefined;
+    // Only replace if this hit is shallower (smaller MRO depth). The local
+    // const lets TS narrow to `number` in the `else` branch so no `!`
+    // assertion is needed.
+    if (firstHit || mroDepth < existingMroDepth) {
         state.signals.typeBindingMroDepth = mroDepth;
         state.tieBreakKey.mroDepth = mroDepth;
     }
     if (def.ownerId === receiverOwner) {
         state.signals.ownerMatch = true;
     }
+    // Pure type-binding candidates (no lexical hit) would otherwise keep the
+    // `ensureCandidate` default `tieBreakKey.origin === 'local'`, making the
+    // Appendix B cascade lump them with local-origin candidates. Demote them
+    // to `'import'` — the strongest non-local origin — only when no earlier
+    // phase set an origin for this candidate. Lexical hits from Step 1 set
+    // `signals.origin` before Step 2 runs, so the guard skips them; Step 3
+    // (`seedFromOwnerScopedContributor`) runs AFTER Step 2 and unconditionally
+    // overrides `tieBreakKey.origin` back to `'local'` for direct-owner
+    // members, so any same-def overlap still ends up ranked correctly.
+    if (firstHit && state.signals.origin === undefined) {
+        state.tieBreakKey.origin = 'import';
+    }
 }
 // ─── Step 3 implementation ─────────────────────────────────────────────────
 function seedFromOwnerScopedContributor(name, contributor, acceptedKinds, perCandidate) {

package/dist/_shared/scope-resolution/registries/lookup-core.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/_shared/scope-resolution/resolve-type-ref.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"resolve-type-ref.d.ts","sourceRoot":"","sources":["../../src/scope-resolution/resolve-type-ref.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAoCG;AAGH,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,KAAK,~~EAAc~~,~~KAAK~~,EAAE,OAAO,EAAE,~~OAAO,EAAE,~~MAAM,YAAY,CAAC;~~AACtE~~,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAC;AAC/C,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAIpE~~;;;;;GAKG;AACH,MAAM,WAAW,WAAW;IAC1B,QAAQ,CAAC,EAAE,EAAE,OAAO,GAAG,KAAK,GAAG,SAAS,CAAC;CAC1C;AAED~~;;;;GAIG;AACH,MAAM,WAAW,qBAAqB;IACpC,QAAQ,CAAC,MAAM,EAAE,WAAW,CAAC;IAC7B,QAAQ,CAAC,QAAQ,EAAE,QAAQ,CAAC;IAC5B,QAAQ,CAAC,kBAAkB,EAAE,kBAAkB,CAAC;CACjD;~~AAsCD~~,wBAAgB,cAAc,CAAC,GAAG,EAAE,OAAO,EAAE,GAAG,EAAE,qBAAqB,GAAG,gBAAgB,GAAG,IAAI,CAgDhG"}
1	+ {"version":3,"file":"resolve-type-ref.d.ts","sourceRoot":"","sources":["../../src/scope-resolution/resolve-type-ref.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAoCG;AAGH,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,KAAK,EAAuB,WAAW,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAC5E,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAC;AAC/C,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAIpE;;;;GAIG;AACH,MAAM,WAAW,qBAAqB;IACpC,QAAQ,CAAC,MAAM,EAAE,WAAW,CAAC;IAC7B,QAAQ,CAAC,QAAQ,EAAE,QAAQ,CAAC;IAC5B,QAAQ,CAAC,kBAAkB,EAAE,kBAAkB,CAAC;CACjD;AA4CD,wBAAgB,cAAc,CAAC,GAAG,EAAE,OAAO,EAAE,GAAG,EAAE,qBAAqB,GAAG,gBAAgB,GAAG,IAAI,CAgDhG"}

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

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/_shared/scope-resolution/shadow/aggregate.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/dist/_shared/scope-resolution/shadow/aggregate.js CHANGED Viewed

@@ -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 ─────────────────────────────────────────────────────────────

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	@@ -1 +1 @@
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package/dist/_shared/scope-resolution/types.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/cli/ai-context.js CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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);