gitnexus 1.6.8-rc.2 → 1.6.8-rc.21

package/scripts/build-tree-sitter-grammars.cjs

@@ -1,19 +1,25 @@
 #!/usr/bin/env node
 /**
- * Activate the vendored tree-sitter native bindings after
- * materialize-vendor-grammars.cjs. One registry-driven script replaces the
- * former per-grammar build-tree-sitter-<name>.cjs files (they were ~95%
- * identical).
+ * Activate the vendored tree-sitter native bindings IN PLACE under `vendor/`.
+ * One registry-driven script replaces the former per-grammar
+ * build-tree-sitter-<name>.cjs files (they were ~95% identical).
+ *
+ * The grammars (tree-sitter-c/dart/proto/swift/kotlin) are loaded from
+ * `vendor/<name>/` by absolute path at runtime (see
+ * src/core/tree-sitter/vendored-grammars.ts) and are NEVER copied into
+ * node_modules — an undeclared package under node_modules is "extraneous" to
+ * every subsequent npm/npx reify, which prunes/relocates it (Windows
+ * `EPERM: …, symlink` + a silent grammar deletion on the 2nd run; #2111/#1728).
  *
  * For each grammar the resolution order is identical:
- *   1. If the package isn't materialized (no binding.gyp) or the binding is
+ *   1. If the vendored source is absent (no binding.gyp) or the binding is
  *      already built, do nothing.
  *   2. Prefer a committed prebuild for this platform-arch (toolchain-free) via
- *      node-gyp-build — the goal once build-tree-sitter-prebuilds.yml has
- *      populated all six tuples.
+ *      node-gyp-build — `vendor/<name>/prebuilds/` ships all six tuples, so on a
+ *      supported platform this returns immediately and writes nothing.
  *   3. Otherwise source-build from the vendored grammar source (binding.gyp +
- *      src/) so parsing still works on any toolchain host — e.g. CI, before the
- *      prebuilds land.
+ *      src/) into `vendor/<name>/build/` (gitignored) so parsing still works on
+ *      a toolchain host that lacks a matching prebuild.
  *
  * HARD INVARIANT: this runs in `gitnexus`'s postinstall, so it MUST NEVER throw
  * or exit non-zero — a failure for any single grammar must not break the install.
@@ -53,7 +59,7 @@ function buildGrammar(short) {
     return;
   }
 
-  const dir = path.join(__dirname, '..', 'node_modules', `tree-sitter-${short}`);
+  const dir = path.join(__dirname, '..', 'vendor', `tree-sitter-${short}`);
   const bindingGyp = path.join(dir, 'binding.gyp');
   const bindingNode = path.join(dir, 'build', 'Release', `tree_sitter_${short}_binding.node`);
 

package/skills/gitnexus-guide.md

@@ -38,6 +38,7 @@ For any task involving code understanding, debugging, impact analysis, or refact
 | `detect_changes` | Git-diff impact — what do your current changes affect                    |
 | `rename`         | Multi-file coordinated rename with confidence-tagged edits               |
 | `cypher`         | Raw graph queries (read `gitnexus://repo/{name}/schema` first)           |
+| `explain`        | Persisted taint findings — source→sink data flows (needs `analyze --pdg`) |
 | `list_repos`     | Discover indexed repos (paginated — `limit`/`offset`)                    |
 
 ### Paginating `list_repos`
@@ -71,6 +72,16 @@ list_repos { offset: 400 }  → repos 401–437,                 hasMore false
 
 Notes: `offset` ≥ `total` returns an empty page (with `total` still reported). Out-of-range or malformed `limit`/`offset` (non-integer, `limit` outside `[1, 200]`, `offset < 0`) are rejected with a clear error — `limit` above the max is rejected, not silently capped. The order is deterministic (lower-cased name, then path), so paging never skips or duplicates an entry while the registry is unchanged.
 
+### Taint findings (`explain`)
+
+`explain` returns intra-procedural taint findings (`TAINTED` edges) recorded by `gitnexus analyze --pdg` — each with a sink category (command-injection, code-injection, path-traversal, sql-injection, xss), source/sink lines, and the ordered hop path with the variable carried on each hop.
+
+- `explain {}` — enumerate all findings for the repo (bounded by `limit`, deterministic order)
+- `explain { target: "src/vuln.ts" }` — findings in a file (suffix path match accepted)
+- `explain { target: "runUserCommand" }` — findings in a function (resolved like `context`; ambiguous names return ranked candidates)
+
+A repo indexed without `--pdg` returns a clear "no taint layer" note. Caveats: findings are intra-procedural only — cross-function, closure/callback, property/field, and implicit flows are not modeled, so the absence of a finding is **not** proof of safety. `SANITIZES` (sanitizer-kill) edges are queryable via `cypher`.
+
 ## Resources Reference
 
 Lightweight reads (~100-500 tokens) for navigation:

package/vendor/tree-sitter-c/package.json

@@ -6,7 +6,7 @@
   "license": "MIT",
   "main": "bindings/node/index.js",
   "types": "bindings/node/index.d.ts",
-  "_vendoredBy": "gitnexus - runtime package derived from tree-sitter-c@0.21.4 (tree-sitter/tree-sitter-c). HELD at 0.21.4 for ABI compatibility with the bundled tree-sitter@0.21.1 runtime (#1242/#858) — do not bump without the runtime upgrade. Vendored because upstream ships native prebuilds for only 4 of 6 platforms (no linux-arm64/win32-arm64, #2116), and tree-sitter-c is a REQUIRED grammar whose source build hard-fails `npm install` on a toolchain-less ARM host. GitNexus cross-builds all six prebuilds via .github/workflows/build-tree-sitter-prebuilds.yml; the C source (binding.gyp + src/) is ALSO vendored so build-tree-sitter-c.cjs can source-build the binding on a toolchain host when no prebuild matches (e.g. CI before prebuilds land). Copied to node_modules/ by materialize-vendor-grammars.cjs (no scripts.install here — #836/#1728).",
+  "_vendoredBy": "gitnexus - runtime package derived from tree-sitter-c@0.21.4 (tree-sitter/tree-sitter-c). HELD at 0.21.4 for ABI compatibility with the bundled tree-sitter@0.21.1 runtime (#1242/#858) — do not bump without the runtime upgrade. Vendored because upstream ships native prebuilds for only 4 of 6 platforms (no linux-arm64/win32-arm64, #2116), and tree-sitter-c is a REQUIRED grammar whose source build hard-fails `npm install` on a toolchain-less ARM host. GitNexus cross-builds all six prebuilds via .github/workflows/build-tree-sitter-prebuilds.yml; the C source (binding.gyp + src/) is ALSO vendored so build-tree-sitter-grammars.cjs can source-build the binding on a toolchain host when no prebuild matches (e.g. CI before prebuilds land). Loaded from vendor/ by absolute path at runtime (vendored-grammars.ts) — NEVER copied to node_modules (#2111) (no scripts.install here — #836/#1728).",
   "peerDependencies": {
     "tree-sitter": "^0.21.0"
   },

package/vendor/tree-sitter-dart/package.json

@@ -6,7 +6,7 @@
   "license": "ISC",
   "main": "bindings/node",
   "types": "bindings/node",
-  "_vendoredBy": "gitnexus - pinned to UserNobody14/tree-sitter-dart commit 80e23c07b64494f7e21090bb3450223ef0b192f4. Copied to node_modules/ by materialize-vendor-grammars.cjs; native build via build-tree-sitter-dart.cjs (#1728, #836).",
+  "_vendoredBy": "gitnexus - pinned to UserNobody14/tree-sitter-dart commit 80e23c07b64494f7e21090bb3450223ef0b192f4. Loaded from vendor/ by absolute path at runtime (vendored-grammars.ts) — NEVER copied to node_modules (#2111); native build via build-tree-sitter-grammars.cjs (#1728, #836).",
   "peerDependencies": {
     "tree-sitter": "^0.21.0"
   },

package/vendor/tree-sitter-kotlin/package.json

@@ -6,7 +6,7 @@
   "license": "MIT",
   "main": "bindings/node/index.js",
   "types": "bindings/node/index.d.ts",
-  "_vendoredBy": "gitnexus - runtime package derived from tree-sitter-kotlin@0.3.8 (fwcd). Unlike Swift's upstream-shipped prebuilds, upstream tree-sitter-kotlin ships SOURCE ONLY (no prebuilds/); the native prebuilds/ here are GitNexus-cross-built by .github/workflows/build-tree-sitter-prebuilds.yml. The grammar source (parser.c/scanner.c/binding.gyp + src/) is ALSO vendored so build-tree-sitter-kotlin.cjs can source-build the binding on a toolchain host when no prebuild matches (e.g. CI before prebuilds land). The generated parser.c is large (~23 MB on disk; it compresses heavily in git); once the prebuilds cover every platform-arch the source serves only as the fallback. Copied to node_modules/ by materialize-vendor-grammars.cjs (no scripts.install here — #836/#1728).",
+  "_vendoredBy": "gitnexus - runtime package derived from tree-sitter-kotlin@0.3.8 (fwcd). Unlike Swift's upstream-shipped prebuilds, upstream tree-sitter-kotlin ships SOURCE ONLY (no prebuilds/); the native prebuilds/ here are GitNexus-cross-built by .github/workflows/build-tree-sitter-prebuilds.yml. The grammar source (parser.c/scanner.c/binding.gyp + src/) is ALSO vendored so build-tree-sitter-grammars.cjs can source-build the binding on a toolchain host when no prebuild matches (e.g. CI before prebuilds land). The generated parser.c is large (~23 MB on disk; it compresses heavily in git); once the prebuilds cover every platform-arch the source serves only as the fallback. Loaded from vendor/ by absolute path at runtime (vendored-grammars.ts) — NEVER copied to node_modules (#2111) (no scripts.install here — #836/#1728).",
   "peerDependencies": {
     "tree-sitter": "^0.21.0"
   },

package/vendor/tree-sitter-proto/package.json

@@ -5,7 +5,7 @@
   "repository": "https://github.com/coder3101/tree-sitter-proto",
   "license": "MIT",
   "main": "bindings/node",
-  "_vendoredBy": "gitnexus — materialized to node_modules/ by materialize-vendor-grammars.cjs; native build via build-tree-sitter-proto.cjs. Do NOT re-add dependencies or an install script (#836, #1728).",
+  "_vendoredBy": "gitnexus — loaded from vendor/ by absolute path at runtime (vendored-grammars.ts) — NEVER copied to node_modules (#2111); native build via build-tree-sitter-grammars.cjs. Do NOT re-add dependencies or an install script (#836, #1728).",
   "peerDependencies": {
     "tree-sitter": ">=0.21.0"
   }

package/vendor/tree-sitter-swift/package.json

@@ -9,7 +9,7 @@
     "type": "git",
     "url": "git+https://github.com/alex-pinkus/tree-sitter-swift.git"
   },
-  "_vendoredBy": "gitnexus - runtime package derived from official tree-sitter-swift@0.7.1 (gitHead 88bfd19a89be9d0481b14566fb6160cccea2fe0a). Unified with Dart/Proto/Kotlin/C: the grammar source (parser.c/scanner.c/binding.gyp + src/) is ALSO vendored so build-tree-sitter-grammars.cjs can source-build the binding on a toolchain host when no prebuild matches (e.g. CI before prebuilds land); src/parser.c is the ABI-14 default (~18 MB on disk, compresses heavily in git — the upstream parser_abi13.c alternate is not vendored). The native prebuilds/ are GitNexus-cross-built by .github/workflows/build-tree-sitter-prebuilds.yml (originally upstream-shipped). Build activation runs via gitnexus/scripts/build-tree-sitter-grammars.cjs after materialize-vendor-grammars.cjs (no scripts.install here — avoids #836 / #1728).",
+  "_vendoredBy": "gitnexus - runtime package derived from official tree-sitter-swift@0.7.1 (gitHead 88bfd19a89be9d0481b14566fb6160cccea2fe0a). Unified with Dart/Proto/Kotlin/C: the grammar source (parser.c/scanner.c/binding.gyp + src/) is ALSO vendored so build-tree-sitter-grammars.cjs can source-build the binding on a toolchain host when no prebuild matches (e.g. CI before prebuilds land); src/parser.c is the ABI-14 default (~18 MB on disk, compresses heavily in git — the upstream parser_abi13.c alternate is not vendored). The native prebuilds/ are GitNexus-cross-built by .github/workflows/build-tree-sitter-prebuilds.yml (originally upstream-shipped). Build activation runs via gitnexus/scripts/build-tree-sitter-grammars.cjs (no scripts.install here — avoids #836 / #1728).",
   "peerDependencies": {
     "tree-sitter": "^0.21.1 || ^0.22.1"
   },

package/web/assets/{agent-CKPMqImC.js → agent-ay4LD70X.js}

@@ -1,4 +1,4 @@
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