gitnexus 1.6.8-rc.2 → 1.6.8-rc.21

package/dist/core/tree-sitter/vendored-grammars.js

@@ -0,0 +1,57 @@
+import { createRequire } from 'node:module';
+import { fileURLToPath } from 'node:url';
+import path from 'node:path';
+const _require = createRequire(import.meta.url);
+/**
+ * Absolute path to the vendored grammar tree (`<pkg>/vendor`).
+ *
+ * This module compiles to `<pkg>/dist/core/tree-sitter/vendored-grammars.js`
+ * and runs from `<pkg>/src/core/tree-sitter/...` under tsx in dev — both sit
+ * three directories below the package root, and the build (`tsc`) never bundles,
+ * so `import.meta.url` resolves the same way in both. `vendor/` ships in the
+ * published package via package.json `files`.
+ */
+export const VENDOR_ROOT = path.resolve(path.dirname(fileURLToPath(import.meta.url)), '..', '..', '..', 'vendor');
+/**
+ * The tree-sitter grammars GitNexus vendors inside its own package (NOT npm
+ * dependencies). Kept in one place so consumers (runtime loaders, the CLI
+ * availability probe, and the test grammar-introspection helper) agree on which
+ * grammars resolve from `vendor/` rather than `node_modules`.
+ */
+export const VENDORED_GRAMMAR_PACKAGES = new Set([
+    'tree-sitter-c',
+    'tree-sitter-dart',
+    'tree-sitter-proto',
+    'tree-sitter-swift',
+    'tree-sitter-kotlin',
+]);
+/** Absolute directory of a vendored grammar package under `vendor/`. */
+export const vendoredGrammarDir = (packageName) => path.join(VENDOR_ROOT, packageName);
+/**
+ * Load a vendored tree-sitter grammar by its absolute path under `vendor/`.
+ *
+ * GitNexus vendors five grammars (c/dart/proto/swift/kotlin) inside its own
+ * package under `vendor/`, each shipping committed per-platform prebuilds. They
+ * are deliberately NOT npm dependencies and must NEVER be copied into
+ * `node_modules`: an undeclared package under `node_modules` is "extraneous" to
+ * every subsequent `npm`/`npx` arborist reify, which prunes or relocates it.
+ * That is the root cause of #2111 / #1728 — on Windows the relocation throws
+ * `EPERM: operation not permitted, symlink` (errno -4048) during the npx-cache
+ * reify Antigravity triggers when it launches the MCP server, and on every OS
+ * the second run silently deletes the materialized grammars.
+ *
+ * Resolving the grammar by absolute path runs its own `bindings/node` entry,
+ * which calls `node-gyp-build(<grammarDir>)` and loads
+ * `vendor/<name>/prebuilds/<platform>-<arch>/…` directly — no build, no write,
+ * no `node_modules` copy. (`node-gyp-build` itself IS an npm dependency and
+ * resolves normally from the grammar directory.)
+ */
+export const requireVendoredGrammar = (packageName) => {
+    // Fail loudly on a name that isn't actually vendored — a typo or a list that
+    // drifted out of sync (VENDORED_GRAMMAR_PACKAGES vs the CLI probe vs the build
+    // registry) would otherwise surface as a confusing absolute-path require miss.
+    if (!VENDORED_GRAMMAR_PACKAGES.has(packageName)) {
+        throw new Error(`'${packageName}' is not a vendored grammar (expected one of: ${[...VENDORED_GRAMMAR_PACKAGES].join(', ')}).`);
+    }
+    return _require(vendoredGrammarDir(packageName));
+};

package/dist/mcp/core/embedder.js

@@ -8,6 +8,7 @@ import { isHttpMode, getHttpDimensions, httpEmbedQuery, } from '../../core/embed
 import { resolveEmbeddingConfig } from '../../core/embeddings/config.js';
 import { applyHfEnvOverrides, isHfDownloadFailure, withHfDownloadRetry, } from '../../core/embeddings/hf-env.js';
 import { getLocalEmbeddingRuntimeBlocker } from '../../core/embeddings/runtime-support.js';
+import { ensureOnnxRuntimeCommonResolvable } from '../../core/embeddings/onnxruntime-common-resolver.js';
 import { silenceStdout, restoreStdout, realStderrWrite } from '../../core/lbug/pool-adapter.js';
 import { logger } from '../../core/logger.js';
 // Model config
@@ -43,6 +44,9 @@ export const initEmbedder = async () => {
         try {
             // Lazy-load transformers.js only after the runtime guard has passed, so
             // unsupported platforms never reach the native ONNX import (#1515).
+            // Under pnpm-strict / `pnpm dlx`, transformers' phantom `onnxruntime-common`
+            // import is unresolvable; register the fallback resolver first (#307).
+            ensureOnnxRuntimeCommonResolvable();
             const { pipeline, env } = await import('@huggingface/transformers');
             env.allowLocalModels = false;
             // Bridge user-controlled env vars to transformers.js: HF_HOME →

package/dist/mcp/local/local-backend.d.ts

@@ -5,7 +5,7 @@
  * Supports multiple indexed repositories via a global registry.
  * LadybugDB connections are opened lazily per repo on first query.
  */
-import { type RegistryEntry } from '../../storage/repo-manager.js';
+import { type RegistryEntry, type BranchSummary } from '../../storage/repo-manager.js';
 import { GroupService } from '../../core/group/service.js';
 /**
  * Quick test-file detection for filtering impact results.
@@ -16,6 +16,15 @@ export declare function isTestFilePath(filePath: string): boolean;
 export declare const VALID_NODE_LABELS: Set<string>;
 /** Valid relation types for impact analysis filtering */
 export declare const VALID_RELATION_TYPES: Set<string>;
+/**
+ * Relation types the #1858 epistemic-boundary probe keys on. Kept as
+ * module-level `readonly` arrays (not Sets) because computeEpistemicBoundary
+ * binds them as Cypher query params (`r.type IN $heritage` / `IN $types`).
+ * The heritage set is exactly the IMPACT_RELATION_CONFIDENCE 0.85 tier —
+ * "statically verifiable, but the concrete binding past it is not".
+ */
+export declare const EPISTEMIC_HERITAGE_RELATION_TYPES: readonly string[];
+export declare const EPISTEMIC_CONSUMER_RELATION_TYPES: readonly string[];
 /**
  * Per-relation-type confidence floor for impact analysis.
  *
@@ -56,6 +65,10 @@ interface RepoHandle {
     lastCommit: string;
     remoteUrl?: string;
     stats?: RegistryEntry['stats'];
+    /** Primary/flat branch name, when known (#2106). */
+    branch?: string;
+    /** Non-primary branch indexes available for this repo (#2106). */
+    branches?: BranchSummary[];
 }
 /**
  * Resolve the git diff cwd for detect_changes, auto-detecting linked worktrees.
@@ -107,6 +120,10 @@ export interface RepoListing {
         path: string;
         lastCommit: string;
     }>;
+    /** Primary/flat branch name, when known (#2106). */
+    branch?: string;
+    /** Non-primary branch indexes available for this repo (#2106). */
+    branches?: Array<Omit<BranchSummary, 'stats'>>;
 }
 /** Continuation metadata for the paginated `list_repos` MCP tool (#2119). */
 export interface ListReposPagination {
@@ -153,6 +170,7 @@ export declare class LocalBackend {
     private initializedRepos;
     private reinitPromises;
     private lastStalenessCheck;
+    private lastObservedIndexedAt;
     private groupToolSvc;
     /**
      * One-shot stderr warnings for sibling-clone drift, keyed by
@@ -214,7 +232,20 @@ export declare class LocalBackend {
      * On a miss, re-reads the registry once in case a new repo was indexed
      * while the MCP server was running.
      */
-    resolveRepo(repoParam?: string): Promise<RepoHandle>;
+    resolveRepo(repoParam?: string, branch?: string): Promise<RepoHandle>;
+    /**
+     * Re-point a resolved repo handle at a specific branch index (#2106).
+     *
+     * - No `branch` (default) → the primary/flat handle, unchanged (backward
+     *   compatible: every existing caller passes no branch).
+     * - `branch` equal to the known primary → the flat handle.
+     * - `branch` matching an indexed non-primary branch → a handle whose
+     *   `lbugPath` points at `branches/<slug>/lbug`; the connection pool keys by
+     *   `lbugPath`, so this is the only change needed to scope every tool.
+     * - `branch` that was never indexed → a clear error (never a silently-empty
+     *   result against the wrong DB).
+     */
+    private applyBranchScope;
     /**
      * Try to resolve a repo from the in-memory cache. Returns null on miss.
      * Throws {@link RegistryAmbiguousTargetError} when `repoParam` matches
@@ -306,6 +337,8 @@ export declare class LocalBackend {
      */
     private maybeWarnSiblingDrift;
     callTool(method: string, params: any): Promise<any>;
+    /** Check repository graph invariants that are suitable for CI gating. */
+    private check;
     /**
      * Query tool — process-grouped search.
      *
@@ -391,6 +424,35 @@ export declare class LocalBackend {
      */
     private context;
     private _contextImpl;
+    /**
+     * Explain tool (#2083 M3 U6) — persisted taint-finding explanation.
+     * WAL-aware wrapper mirroring `context`.
+     */
+    private explain;
+    /**
+     * Taint findings are persisted as `TAINTED` rows in CodeRelation whose
+     * endpoints are BOTH BasicBlock nodes — the label anchor restricts every
+     * query here to the BasicBlock→BasicBlock partition of the rel table
+     * (which holds only the sparse, per-function-capped pdg layers), never a
+     * global symbol-space scan (the S1 verdict; LadybugDB has no rel-property
+     * index, so the label anchor IS the bound).
+     *
+     * Anchoring granularity:
+     * - file target → BasicBlock id prefix (`BasicBlock:<filePath>:` — the
+     *   shared `basicBlockId` template) with an exact-or-suffix path match so
+     *   `vuln.ts` finds `src/vuln.ts`.
+     * - symbol target → resolved via `resolveSymbolCandidates` (the context()
+     *   path: ambiguous ⇒ ranked candidates, unknown ⇒ not-found), then the
+     *   file id-prefix PLUS source-block startLine within the symbol's
+     *   [startLine, endLine] span. Findings are intra-procedural, so filtering
+     *   the SOURCE endpoint is sufficient — both endpoints share the function.
+     *   Symbols without a line span degrade to the file-level filter.
+     *
+     * The per-finding `sinkKind` and hop path decode from the persisted
+     * `reason` via the SHARED `taint/path-codec.ts` (the U4 write path encodes
+     * with the same module — `;<kind>` header + ordered `variable:line` hops).
+     */
+    private _explainImpl;
     /**
      * Legacy explore — kept for backwards compatibility with resources.ts.
      * Routes cluster/process types to direct graph queries.
@@ -409,6 +471,28 @@ export declare class LocalBackend {
     private rename;
     private impact;
     private _impactImpl;
+    /**
+     * #1858 — epistemic lower-bound detection.
+     *
+     * impact()/context() traverse only edges materialized in the graph. When the
+     * queried symbol sits on an interface / abstract boundary, callers that bind
+     * to the interface via DI, a container, or dynamic dispatch — rather than
+     * naming the concrete symbol — are not traced. The reported count is then a
+     * lower bound, not an exact figure. Instead of returning a confident count
+     * that silently omits those callers, annotate the result with
+     * `epistemic: 'lower-bound'` plus a human-readable boundary note. A fully
+     * resolved leaf with no indirection stays `epistemic: 'exact'`.
+     *
+     * Aligns with the numeric confidence model rather than the long-deleted
+     * TIER_CONFIDENCE enum: the heritage/indirection edges this keys on
+     * (IMPLEMENTS / METHOD_IMPLEMENTS / EXTENDS) carry the 0.85
+     * `IMPACT_RELATION_CONFIDENCE` floor — "statically verifiable, but the
+     * concrete binding past it is not".
+     *
+     * Never throws: on query error it returns 'exact', so it can only add signal,
+     * never suppress a result.
+     */
+    private computeEpistemicBoundary;
     /**
      * Shared BFS traversal for impact analysis (name-resolved or UID-resolved symbol).
      */