fix(sync): apply ignore matcher to git change-detection fast path (#766)

CHANGELOG.md

@@ -41,6 +41,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 - Symbols defined in Svelte and Vue `<script>` blocks were reported one line below where they actually are — a function on line 3 was reported at line 4 — which offset every script-block symbol's location in search, `codegraph_node`, and explore output. Line numbers now match the file exactly. Re-index a project to benefit. (Svelte, Vue)
 - Doc comments are now captured for exported, `const`-assigned, and decorated declarations, and the documentation a symbol carries is now clean across every supported language. Previously a comment above `export class X`, `export const fn = () => …`, a plain `const fn = () => …`, or a decorated Python `def`/`class` (`@app.route(...)`, `@dataclass`) was dropped entirely — only comments directly above a plain declaration were kept. CodeGraph now finds the comment through the `export` / `const` / decorator wrapper. Comment-marker cleanup was also rounded out for every language CodeGraph supports: Rust/Swift/Kotlin doc lines (`///`, `//!`), Python/Ruby/shell `#`, Lua/Luau (`--` and `--[[ ]]`), and Pascal (`{ }` and `(* *)`) no longer leave stray markers in the stored text — validated end-to-end across all 19 code languages plus Svelte/Vue `<script>` blocks. (#780). Thanks @caleb-kaiser.
+- `codegraph status` no longer reports a perpetual pending change for a file inside a committed dependency or build directory (for example `vendor/` or `node_modules/`) that the index deliberately excludes. Editing such a tracked-but-excluded file showed up as a pending addition that no `codegraph sync` or `codegraph index` could ever clear, because indexing correctly skips those directories — so `status` and a full re-index disagreed forever. Change detection now applies the same exclusion rules as indexing. Thanks @monochrome3694. (#766)
 - Go method calls made through a chained factory function now resolve to the correct type. A call like `New().Method()` used to drop the receiver, so the chained method attached to a same-named method on an unrelated type — or didn't resolve. CodeGraph now captures Go return types (a pointer `*Foo` resolves to `Foo`, and a multi-return `(*Foo, error)` to its first result), infers the chained receiver's type from what the factory function returns, and resolves the method on it — including methods promoted from an embedded struct — creating the edge only when the type or an embedded type genuinely has the method. Existing Go indexes should be re-indexed (`codegraph index -f`) to benefit. (#750) (Go)
 - Scala method calls made through a companion-object factory, a fluent chain, or a case-class `apply` now resolve to the correct type. A call like `Foo.create().bar()` or `Builder(cfg).bar()` used to drop the receiver, so the chained method silently attached to a same-named method on an unrelated type — most often mis-attributing a standard-library `Option` / `Iterator` `.map` / `.flatMap` / `.foreach` onto your own same-named class. CodeGraph now captures Scala return types (a generic `List[Foo]` resolves to its container `List`, a qualified `pkg.Foo` to `Foo`), infers the chained receiver's type from what the inner call returns or constructs, and resolves the method on it — including methods inherited from a trait the type extends — creating the edge only when that type or one of its traits genuinely has the method (so a wrong inference produces no edge instead of a misleading one). Existing Scala indexes should be re-indexed (`codegraph index -f`) to benefit. (#750) (Scala)
 - Rust method calls made through a chained associated function now resolve to the correct type. A call like `Foo::new().bar()` or `Foo::with(cfg).build()` used to drop the receiver, so the chained method silently attached to a same-named method on an unrelated type — or didn't resolve. CodeGraph now captures Rust return types (`-> Self` resolves to the implementing type), infers the chained receiver's type from what the associated function returns, and resolves the method on it — including methods provided by a trait the type implements (via the new `impl Trait for Type` relationships) — creating the edge only when the type or one of its traits genuinely has the method. Existing Rust indexes should be re-indexed (`codegraph index -f`) to benefit. (#750) (Rust)

__tests__/sync.test.ts

@@ -302,5 +302,35 @@ describe('Sync Module', () => {
       expect(result.filesRemoved).toBe(0);
       expect(result.changedFilePaths).toBeUndefined();
     });
+
+    it('should not report changes to excluded tracked files (issue #766)', () => {
+      // A committed dependency dir (e.g. vendor/) is excluded from the index by
+      // the built-in default ignores, even though its files are tracked in git.
+      // git status still reports working-tree changes there, but the git
+      // fast-path of change detection must apply the same ignore matcher as
+      // enumeration — otherwise status flags a pending change that `index` will
+      // never produce (a perpetual phantom add that no sync can clear).
+      const vendorDir = path.join(testDir, 'vendor');
+      fs.mkdirSync(vendorDir);
+      fs.writeFileSync(path.join(vendorDir, 'lib.ts'), `export function vendored() { return 1; }`);
+      git('add', '-A');
+      git('commit', '-m', 'add vendored dep');
+
+      // Modify the tracked-but-excluded file → git status now flags it...
+      fs.writeFileSync(path.join(vendorDir, 'lib.ts'), `export function vendored() { return 2; }`);
+      // ...alongside a genuine change to real source code.
+      fs.writeFileSync(
+        path.join(testDir, 'src', 'index.ts'),
+        `export function hello() { return 'changed'; }`
+      );
+
+      const changes = cg.getChangedFiles();
+
+      // The excluded file must not leak into change detection...
+      expect(changes.added).not.toContain('vendor/lib.ts');
+      expect(changes.modified).not.toContain('vendor/lib.ts');
+      // ...while the genuine source change is still detected.
+      expect(changes.modified).toContain('src/index.ts');
+    });
   });
 });

src/extraction/index.ts

@@ -1540,11 +1540,22 @@ export class ExtractionOrchestrator {
         }
       }
 
+      // Apply the same ignore matcher as enumeration (getGitVisibleFiles). git
+      // status reports working-tree changes to tracked files inside committed
+      // dependency/build dirs (vendor/, node_modules/, …) that the index
+      // deliberately excludes — without this filter those leak into `added`,
+      // disagreeing with what `index` produces (a phantom change no sync clears).
+      // Deletions stay unfiltered: they only act on paths already in the DB,
+      // where removal is always correct (and lets a now-excluded dir's stale
+      // entries clean up). (See issue #766.)
+      const ignoreMatcher = buildDefaultIgnore(this.rootDir);
+
       // Modified + added files — read + hash, compare with DB. Untracked (`??`)
       // files stay untracked in git even after indexing, so they must be
       // hash-compared like modified files instead of always counting as added —
       // otherwise status reports them as pending forever. (See issue #206.)
       for (const filePath of [...gitChanges.modified, ...gitChanges.added]) {
+        if (ignoreMatcher.ignores(filePath)) continue;
         const fullPath = path.join(this.rootDir, filePath);
         let content: string;
         try {