@colbymchenry/codegraph-darwin-x64 0.9.4 → 0.9.6

package/lib/dist/extraction/grammars.js

@@ -83,6 +83,7 @@ const WASM_GRAMMAR_FILES = {
     scala: 'tree-sitter-scala.wasm',
     lua: 'tree-sitter-lua.wasm',
     luau: 'tree-sitter-luau.wasm',
+    objc: 'tree-sitter-objc.wasm',
 };
 /**
  * File extension to Language mapping
@@ -137,6 +138,15 @@ exports.EXTENSION_MAP = {
     '.sc': 'scala',
     '.lua': 'lua',
     '.luau': 'luau',
+    '.m': 'objc',
+    '.mm': 'objc',
+    // XML: file-level tracking; the MyBatis extractor matches `<mapper namespace="...">`
+    // shape and emits SQL-statement nodes (other XML returns empty).
+    '.xml': 'xml',
+    // Spring config: `application.properties` / `application-*.properties`. Same
+    // shape as the `.yml` variants — the YAML/properties extractor emits one node
+    // per leaf key, and the Spring resolver links `@Value("${k}")` references.
+    '.properties': 'properties',
 };
 /**
  * Whether a file is one CodeGraph can parse, based purely on its extension.
@@ -256,10 +266,12 @@ function detectLanguage(filePath, source) {
         return 'yaml';
     const ext = filePath.substring(filePath.lastIndexOf('.')).toLowerCase();
     const lang = exports.EXTENSION_MAP[ext] || 'unknown';
-    // .h files could be C or C++ — check source content for C++ features
+    // .h files could be C, C++, or Objective-C — check source content
     if (lang === 'c' && ext === '.h' && source) {
         if (looksLikeCpp(source))
             return 'cpp';
+        if (looksLikeObjc(source))
+            return 'objc';
     }
     return lang;
 }
@@ -271,6 +283,13 @@ function looksLikeCpp(source) {
     const sample = source.substring(0, 8192);
     return /\bnamespace\b|\bclass\s+\w+\s*[:{]|\btemplate\s*<|\b(?:public|private|protected)\s*:|\bvirtual\b|\busing\s+(?:namespace\b|\w+\s*=)/.test(sample);
 }
+/**
+ * Heuristic: does a .h file contain Objective-C constructs?
+ */
+function looksLikeObjc(source) {
+    const sample = source.substring(0, 8192);
+    return /@(?:interface|implementation|protocol|synthesize)\b/.test(sample);
+}
 /**
  * Check if a language is supported (has a grammar defined).
  * Returns true if the grammar exists, even if not yet loaded.
@@ -286,6 +305,10 @@ function isLanguageSupported(language) {
         return true; // file-level tracking only; Drupal routing extraction via framework resolver
     if (language === 'twig')
         return true; // file-level tracking only
+    if (language === 'xml')
+        return true; // MyBatis mapper extractor
+    if (language === 'properties')
+        return true; // Spring config keys
     if (language === 'unknown')
         return false;
     return language in WASM_GRAMMAR_FILES;
@@ -298,6 +321,8 @@ function isGrammarLoaded(language) {
         return true;
     if (language === 'yaml' || language === 'twig')
         return true; // no WASM grammar needed
+    if (language === 'xml' || language === 'properties')
+        return true; // no WASM grammar needed
     return languageCache.has(language);
 }
 /**
@@ -370,8 +395,11 @@ function getLanguageDisplayName(language) {
         scala: 'Scala',
         lua: 'Lua',
         luau: 'Luau',
+        objc: 'Objective-C',
         yaml: 'YAML',
         twig: 'Twig',
+        xml: 'XML',
+        properties: 'Java properties',
         unknown: 'Unknown',
     };
     return names[language] || language;

package/lib/dist/extraction/grammars.js.map

@@ -1 +1 @@
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+{"version":3,"file":"grammars.js","sourceRoot":"","sources":["../../src/extraction/grammars.ts"],"names":[],"mappings":";AAAA;;;;;;GAMG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAyGH,oCAKC;AAOD,4CAMC;AAgBD,oCAMC;AAOD,4DAkCC;AAMD,0CAGC;AAKD,sDAEC;AAMD,8BAcC;AAKD,wCAcC;AAuBD,kDAUC;AAKD,0CAKC;AAKD,sDAEC;AASD,kCAMC;AAKD,4CAQC;AAKD,kEAMC;AAKD,wDAiCC;AA9WD,2CAA6B;AAC7B,qDAAmE;AAKnE;;;GAGG;AACH,MAAM,kBAAkB,GAAoC;IAC1D,UAAU,EAAE,6BAA6B;IACzC,GAAG,EAAE,sBAAsB;IAC3B,UAAU,EAAE,6BAA6B;IACzC,GAAG,EAAE,6BAA6B;IAClC,MAAM,EAAE,yBAAyB;IACjC,EAAE,EAAE,qBAAqB;IACzB,IAAI,EAAE,uBAAuB;IAC7B,IAAI,EAAE,uBAAuB;IAC7B,CAAC,EAAE,oBAAoB;IACvB,GAAG,EAAE,sBAAsB;IAC3B,MAAM,EAAE,0BAA0B;IAClC,GAAG,EAAE,sBAAsB;IAC3B,IAAI,EAAE,uBAAuB;IAC7B,KAAK,EAAE,wBAAwB;IAC/B,MAAM,EAAE,yBAAyB;IACjC,IAAI,EAAE,uBAAuB;IAC7B,MAAM,EAAE,yBAAyB;IACjC,KAAK,EAAE,wBAAwB;IAC/B,GAAG,EAAE,sBAAsB;IAC3B,IAAI,EAAE,uBAAuB;IAC7B,IAAI,EAAE,uBAAuB;CAC9B,CAAC;AAEF;;GAEG;AACU,QAAA,aAAa,GAA6B;IACrD,KAAK,EAAE,YAAY;IACnB,MAAM,EAAE,KAAK;IACb,KAAK,EAAE,YAAY;IACnB,MAAM,EAAE,YAAY;IACpB,MAAM,EAAE,YAAY;IACpB,MAAM,EAAE,KAAK;IACb,KAAK,EAAE,QAAQ;IACf,MAAM,EAAE,QAAQ;IAChB,KAAK,EAAE,IAAI;IACX,KAAK,EAAE,MAAM;IACb,OAAO,EAAE,MAAM;IACf,IAAI,EAAE,GAAG;IACT,IAAI,EAAE,GAAG,EAAE,qCAAqC;IAChD,MAAM,EAAE,KAAK;IACb,KAAK,EAAE,KAAK;IACZ,MAAM,EAAE,KAAK;IACb,MAAM,EAAE,KAAK;IACb,MAAM,EAAE,KAAK;IACb,KAAK,EAAE,QAAQ;IACf,MAAM,EAAE,KAAK;IACb,sCAAsC;IACtC,SAAS,EAAE,KAAK;IAChB,UAAU,EAAE,KAAK;IACjB,QAAQ,EAAE,KAAK;IACf,MAAM,EAAE,KAAK;IACb,uFAAuF;IACvF,MAAM,EAAE,MAAM;IACd,OAAO,EAAE,MAAM;IACf,kEAAkE;IAClE,OAAO,EAAE,MAAM;IACf,KAAK,EAAE,MAAM;IACb,OAAO,EAAE,MAAM;IACf,QAAQ,EAAE,OAAO;IACjB,KAAK,EAAE,QAAQ;IACf,MAAM,EAAE,QAAQ;IAChB,OAAO,EAAE,MAAM;IACf,SAAS,EAAE,QAAQ;IACnB,SAAS,EAAE,QAAQ;IACnB,MAAM,EAAE,KAAK;IACb,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,QAAQ,EAAE,OAAO;IACjB,KAAK,EAAE,OAAO;IACd,MAAM,EAAE,KAAK;IACb,OAAO,EAAE,MAAM;IACf,IAAI,EAAE,MAAM;IACZ,KAAK,EAAE,MAAM;IACb,qFAAqF;IACrF,iEAAiE;IACjE,MAAM,EAAE,KAAK;IACb,6EAA6E;IAC7E,8EAA8E;IAC9E,2EAA2E;IAC3E,aAAa,EAAE,YAAY;CAC5B,CAAC;AAEF;;;;GAIG;AACH,SAAgB,YAAY,CAAC,QAAgB;IAC3C,IAAI,gBAAgB,CAAC,QAAQ,CAAC;QAAE,OAAO,IAAI,CAAC,CAAC,sCAAsC;IACnF,MAAM,GAAG,GAAG,QAAQ,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,GAAG,GAAG,CAAC;QAAE,OAAO,KAAK,CAAC;IAC1B,OAAO,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,IAAI,qBAAa,CAAC;AAC5D,CAAC;AAED;;;;GAIG;AACH,SAAgB,gBAAgB,CAAC,QAAgB;IAC/C,OAAO,CACL,QAAQ,KAAK,aAAa;QAC1B,QAAQ,CAAC,QAAQ,CAAC,cAAc,CAAC;QACjC,QAAQ,CAAC,QAAQ,CAAC,SAAS,CAAC,CAC7B,CAAC;AACJ,CAAC;AAED;;GAEG;AACH,MAAM,WAAW,GAAG,IAAI,GAAG,EAAoB,CAAC;AAChD,MAAM,aAAa,GAAG,IAAI,GAAG,EAA0B,CAAC;AACxD,MAAM,wBAAwB,GAAG,IAAI,GAAG,EAAoB,CAAC;AAE7D,IAAI,iBAAiB,GAAG,KAAK,CAAC;AAE9B;;;;GAIG;AACI,KAAK,UAAU,YAAY;IAChC,IAAI,iBAAiB;QAAE,OAAO;IAE9B,MAAM,wBAAM,CAAC,IAAI,EAAE,CAAC;IAEpB,iBAAiB,GAAG,IAAI,CAAC;AAC3B,CAAC;AAED;;;;GAIG;AACI,KAAK,UAAU,wBAAwB,CAAC,SAAqB;IAClE,IAAI,CAAC,iBAAiB,EAAE,CAAC;QACvB,MAAM,YAAY,EAAE,CAAC;IACvB,CAAC;IAED,wFAAwF;IACxF,MAAM,MAAM,GAAG,CAAC,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAC3C,CAAC,IAAI,EAA2B,EAAE,CAChC,IAAI,IAAI,kBAAkB;QAC1B,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC;QACxB,CAAC,wBAAwB,CAAC,GAAG,CAAC,IAAI,CAAC,CACtC,CAAC;IAEF,sFAAsF;IACtF,8DAA8D;IAC9D,KAAK,MAAM,IAAI,IAAI,MAAM,EAAE,CAAC;QAC1B,MAAM,QAAQ,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAC;QAC1C,IAAI,CAAC;YACH,uEAAuE;YACvE,uEAAuE;YACvE,wEAAwE;YACxE,sEAAsE;YACtE,2CAA2C;YAC3C,MAAM,QAAQ,GAAG,CAAC,IAAI,KAAK,QAAQ,IAAI,IAAI,KAAK,OAAO,IAAI,IAAI,KAAK,KAAK,IAAI,IAAI,KAAK,MAAM,CAAC;gBAC3F,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,MAAM,EAAE,QAAQ,CAAC;gBACxC,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,yBAAyB,QAAQ,EAAE,CAAC,CAAC;YACzD,MAAM,QAAQ,GAAG,MAAM,0BAAY,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;YACnD,aAAa,CAAC,GAAG,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC;QACpC,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,OAAO,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACvE,OAAO,CAAC,IAAI,CAAC,8BAA8B,IAAI,2CAA2C,OAAO,EAAE,CAAC,CAAC;YACrG,wBAAwB,CAAC,GAAG,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;QAC9C,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;GAGG;AACI,KAAK,UAAU,eAAe;IACnC,MAAM,YAAY,GAAG,MAAM,CAAC,IAAI,CAAC,kBAAkB,CAAsB,CAAC;IAC1E,MAAM,wBAAwB,CAAC,YAAY,CAAC,CAAC;AAC/C,CAAC;AAED;;GAEG;AACH,SAAgB,qBAAqB;IACnC,OAAO,iBAAiB,CAAC;AAC3B,CAAC;AAED;;;GAGG;AACH,SAAgB,SAAS,CAAC,QAAkB;IAC1C,IAAI,WAAW,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC9B,OAAO,WAAW,CAAC,GAAG,CAAC,QAAQ,CAAE,CAAC;IACpC,CAAC;IAED,MAAM,IAAI,GAAG,aAAa,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;IACzC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,IAAI,CAAC;IACd,CAAC;IAED,MAAM,MAAM,GAAG,IAAI,wBAAM,EAAE,CAAC;IAC5B,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC;IACzB,WAAW,CAAC,GAAG,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;IAClC,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;GAEG;AACH,SAAgB,cAAc,CAAC,QAAgB,EAAE,MAAe;IAC9D,4EAA4E;IAC5E,wDAAwD;IACxD,IAAI,gBAAgB,CAAC,QAAQ,CAAC;QAAE,OAAO,MAAM,CAAC;IAC9C,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,QAAQ,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC;IACxE,MAAM,IAAI,GAAG,qBAAa,CAAC,GAAG,CAAC,IAAI,SAAS,CAAC;IAE7C,kEAAkE;IAClE,IAAI,IAAI,KAAK,GAAG,IAAI,GAAG,KAAK,IAAI,IAAI,MAAM,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package/lib/dist/extraction/index.d.ts

@@ -6,6 +6,7 @@
 import * as fs from 'fs';
 import { ExtractionResult, ExtractionError } from '../types';
 import { QueryBuilder } from '../db/queries';
+import { Ignore } from 'ignore';
 /**
  * Progress callback for indexing operations
  */
@@ -44,6 +45,14 @@ export interface SyncResult {
  * Calculate SHA256 hash of file contents
  */
 export declare function hashContent(content: string): string;
+/**
+ * An `ignore` matcher seeded with the built-in defaults, merged with the project's
+ * root .gitignore so a negation there (e.g. `!vendor/`) overrides a default. Shared
+ * by both enumeration paths so behavior is identical with or without git — and so
+ * the defaults apply to tracked files too (committing a dependency dir doesn't make
+ * it project code; the explicit `.gitignore` negation is the only opt-in).
+ */
+export declare function buildDefaultIgnore(rootDir: string): Ignore;
 /**
  * Recursively scan a directory for source files.
  *
@@ -106,8 +115,12 @@ export declare class ExtractionOrchestrator {
      */
     private storeExtractionResult;
     /**
-     * Sync with current file state.
-     * Uses git status as a fast path when available, falling back to full scan.
+     * Sync the index with the current file state.
+     *
+     * Change detection is filesystem-based, never git: a (size, mtime) stat
+     * pre-filter skips unchanged files, then a content-hash compare confirms real
+     * changes. This works in non-git projects and catches committed changes from
+     * `git pull`/`checkout`/`merge`/`rebase` that `git status` cannot see.
      */
     sync(onProgress?: (progress: IndexProgress) => void): Promise<SyncResult>;
     /**

package/lib/dist/extraction/index.d.ts.map

@@ -1 +1 @@
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package/lib/dist/extraction/index.js

@@ -43,6 +43,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.loadAllGrammars = exports.loadGrammarsForLanguages = exports.initGrammars = exports.getSupportedLanguages = exports.isGrammarLoaded = exports.isLanguageSupported = exports.isSourceFile = exports.detectLanguage = exports.extractFromSource = exports.ExtractionOrchestrator = void 0;
 exports.hashContent = hashContent;
+exports.buildDefaultIgnore = buildDefaultIgnore;
 exports.scanDirectory = scanDirectory;
 exports.scanDirectoryAsync = scanDirectoryAsync;
 const fs = __importStar(require("fs"));
@@ -88,6 +89,83 @@ function hashContent(content) {
  * symbols. 1 MB covers essentially all hand-written source.
  */
 const MAX_FILE_SIZE = 1024 * 1024;
+/**
+ * Directory names that are dependency, build, cache, or tooling output across the
+ * languages/frameworks CodeGraph supports — curated from the canonical
+ * github/gitignore templates. Excluded by default so the graph reflects your code,
+ * not third-party noise, without requiring a `.gitignore` (issue #407). The
+ * exclusion applies uniformly (git or not, tracked or not); the only opt-in is an
+ * explicit `.gitignore` negation (e.g. `!vendor/`). First-party-prone or generic
+ * names (`packages`, `lib`, `app`, `bin`, `src`, `deps`, `env`, `tmp`, `storage`,
+ * `Library`) are deliberately NOT listed, to avoid ever hiding real source.
+ *
+ * Only dirs that actually contain *indexable source* (or are enormous) earn a slot
+ * — IDE/state dirs like `.idea`/`.vs` are omitted because CodeGraph indexes only
+ * recognized source extensions, so they produce no symbols regardless.
+ */
+const DEFAULT_IGNORE_DIRS = new Set([
+    // JS / TS — dependency directories
+    'node_modules', 'bower_components', 'jspm_packages', 'web_modules',
+    '.yarn', '.pnpm-store',
+    // JS / TS — framework & bundler build / cache / deploy output
+    '.next', '.nuxt', '.svelte-kit', '.turbo', '.vite', '.parcel-cache', '.angular',
+    '.docusaurus', 'storybook-static', '.vinxi', '.nitro', 'out-tsc',
+    '.vercel', '.netlify', '.wrangler',
+    // Build output (common across ecosystems)
+    'dist', 'build', 'out', '.output',
+    // Test / coverage
+    'coverage', '.nyc_output',
+    // Python
+    '__pycache__', '__pypackages__', '.venv', 'venv', '.pixi', '.pdm-build',
+    '.mypy_cache', '.pytest_cache', '.ruff_cache', '.tox', '.nox', '.hypothesis',
+    '.ipynb_checkpoints', '.eggs',
+    // Rust / JVM (Maven, Gradle, Scala)
+    'target', '.gradle',
+    // .NET
+    'obj',
+    // Vendored deps (Go, PHP/Composer, Ruby/Bundler)
+    'vendor',
+    // Swift / iOS
+    '.build', 'Pods', 'Carthage', 'DerivedData', '.swiftpm',
+    // Dart / Flutter
+    '.dart_tool', '.pub-cache',
+    // Native (Android NDK, C/C++ deps)
+    '.cxx', '.externalNativeBuild', 'vcpkg_installed',
+    // Scala tooling
+    '.bloop', '.metals',
+    // Lua / Luau (LuaRocks)
+    'lua_modules', '.luarocks',
+    // Delphi / RAD Studio IDE backups (duplicate .pas source — would double-count)
+    '__history', '__recovery',
+    // Generic cache
+    '.cache',
+]);
+/** Gitignore-style patterns for the `ignore` matcher: the dirs above plus a few globs. */
+const DEFAULT_IGNORE_PATTERNS = [
+    ...Array.from(DEFAULT_IGNORE_DIRS, (d) => `${d}/`),
+    '*.egg-info/', // Python packaging metadata
+    'cmake-build-*/', // CLion / CMake build trees
+    'bazel-*/', // Bazel output symlink trees
+];
+/**
+ * An `ignore` matcher seeded with the built-in defaults, merged with the project's
+ * root .gitignore so a negation there (e.g. `!vendor/`) overrides a default. Shared
+ * by both enumeration paths so behavior is identical with or without git — and so
+ * the defaults apply to tracked files too (committing a dependency dir doesn't make
+ * it project code; the explicit `.gitignore` negation is the only opt-in).
+ */
+function buildDefaultIgnore(rootDir) {
+    const ig = (0, ignore_1.default)().add(DEFAULT_IGNORE_PATTERNS);
+    try {
+        const rootGitignore = path.join(rootDir, '.gitignore');
+        if (fs.existsSync(rootGitignore))
+            ig.add(fs.readFileSync(rootGitignore, 'utf-8'));
+    }
+    catch {
+        // Unreadable root .gitignore — the built-in defaults still apply.
+    }
+    return ig;
+}
 /**
  * Collect git-visible files (tracked + untracked, .gitignore-respected) from the
  * git repository rooted at `repoDir`, adding each to `files` with `prefix`
@@ -161,7 +239,11 @@ function getGitVisibleFiles(rootDir) {
         }
         const files = new Set();
         collectGitFiles(rootDir, '', files);
-        return files;
+        // Apply built-in default ignores uniformly — to tracked files too, since
+        // committing a dependency/build dir doesn't make it project code. A
+        // `.gitignore` negation (e.g. `!vendor/`) is the explicit opt-in. (issue #407)
+        const ig = buildDefaultIgnore(rootDir);
+        return new Set([...files].filter((f) => !ig.ignores(f)));
     }
     catch {
         return null;
@@ -297,7 +379,9 @@ function scanDirectoryWalk(rootDir, onProgress) {
         }
         visitedDirs.add(realDir);
         // This directory's own .gitignore (if present) applies to everything below it.
-        const own = loadIgnore(dir);
+        // The root's .gitignore is already merged into the seeded base matcher (so a
+        // negation there can override a built-in default), so skip it here.
+        const own = dir === rootDir ? null : loadIgnore(dir);
         const active = own ? [...matchers, own] : matchers;
         let entries;
         try {
@@ -349,7 +433,9 @@ function scanDirectoryWalk(rootDir, onProgress) {
             }
         }
     }
-    walk(rootDir, []);
+    // Seed a base matcher with the built-in default ignores (merged with the root
+    // .gitignore so a negation can override). Nested .gitignores still layer per-dir.
+    walk(rootDir, [{ dir: rootDir, ig: buildDefaultIgnore(rootDir) }]);
     return files;
 }
 /**
@@ -408,6 +494,24 @@ class ExtractionOrchestrator {
                     return null;
                 }
             },
+            // Monorepo support — needed by framework detect()s that probe
+            // subpackage manifests (e.g. fabric-view looking at
+            // packages/<sub>/package.json when the root manifest is just a
+            // workspace declaration). Matches the resolver-context shape.
+            listDirectories: (relativePath) => {
+                const target = relativePath === '.' || relativePath === ''
+                    ? rootDir
+                    : path.join(rootDir, relativePath);
+                try {
+                    return fs
+                        .readdirSync(target, { withFileTypes: true })
+                        .filter((entry) => entry.isDirectory())
+                        .map((entry) => entry.name);
+                }
+                catch {
+                    return [];
+                }
+            },
         };
     }
     /**
@@ -1053,8 +1157,12 @@ class ExtractionOrchestrator {
         this.queries.upsertFile(fileRecord);
     }
     /**
-     * Sync with current file state.
-     * Uses git status as a fast path when available, falling back to full scan.
+     * Sync the index with the current file state.
+     *
+     * Change detection is filesystem-based, never git: a (size, mtime) stat
+     * pre-filter skips unchanged files, then a content-hash compare confirms real
+     * changes. This works in non-git projects and catches committed changes from
+     * `git pull`/`checkout`/`merge`/`rebase` that `git status` cannot see.
      */
     async sync(onProgress) {
         await (0, grammars_1.initGrammars)(); // Initialize WASM runtime (grammars loaded lazily below)
@@ -1071,88 +1179,72 @@ class ExtractionOrchestrator {
             total: 0,
         });
         const filesToIndex = [];
-        const gitChanges = getGitChangedFiles(this.rootDir);
-        if (gitChanges) {
-            // === Git fast path ===
-            // Only inspect the files git reports as changed instead of scanning everything.
-            filesChecked = gitChanges.modified.length + gitChanges.added.length + gitChanges.deleted.length;
-            // Handle deleted files
-            for (const filePath of gitChanges.deleted) {
-                const tracked = this.queries.getFileByPath(filePath);
-                if (tracked) {
-                    this.queries.deleteFile(filePath);
-                    filesRemoved++;
-                }
+        // === Filesystem reconcile (git-independent) ===
+        // The source of truth for "what changed" is the filesystem vs the indexed
+        // state — never git. We enumerate the current source files and reconcile
+        // each against the DB. A cheap (size, mtime) stat pre-filter skips unchanged
+        // files without reading or hashing them, so the expensive read+hash+parse
+        // only runs for files that actually changed. This catches edits/adds/deletes
+        // whether or not the project uses git, and crucially also catches committed
+        // changes from `git pull`/`checkout`/`merge`/`rebase` — which `git status`
+        // cannot see, because the working tree is clean afterward.
+        const currentFiles = scanDirectory(this.rootDir);
+        filesChecked = currentFiles.length;
+        const currentSet = new Set(currentFiles);
+        const trackedFiles = this.queries.getAllFiles();
+        const trackedMap = new Map();
+        for (const f of trackedFiles) {
+            trackedMap.set(f.path, f);
+        }
+        // Removals: tracked in the DB but no longer a present source file. Check the
+        // filesystem directly — `scanDirectory` (via `git ls-files`) still lists a
+        // file deleted from disk but not yet staged, so set membership alone misses it.
+        for (const tracked of trackedFiles) {
+            if (!currentSet.has(tracked.path) || !fs.existsSync(path.join(this.rootDir, tracked.path))) {
+                this.queries.deleteFile(tracked.path);
+                filesRemoved++;
             }
-            // Handle modified + added files — read + hash only these. Untracked
-            // (`??`) files stay untracked in git even after we index them, so they
-            // can't be trusted as "new": re-hash and compare against the DB exactly
-            // like modified files. Otherwise every sync re-indexes them and status
-            // reports them as pending forever. (See issue #206.)
-            for (const filePath of [...gitChanges.modified, ...gitChanges.added]) {
-                const fullPath = path.join(this.rootDir, filePath);
-                let content;
+        }
+        // Adds / modifications.
+        for (const filePath of currentFiles) {
+            const fullPath = path.join(this.rootDir, filePath);
+            const tracked = trackedMap.get(filePath);
+            // Cheap pre-filter: an already-indexed file whose size AND mtime both match
+            // the DB is unchanged — skip it without reading or hashing. (A content
+            // change that preserves both exactly is the blind spot every mtime-based
+            // incremental tool accepts; `index --force` is the escape hatch. Git bumps
+            // mtime on every file it writes during checkout/merge, so pulls are caught.)
+            if (tracked) {
                 try {
-                    content = fs.readFileSync(fullPath, 'utf-8');
+                    const stat = fs.statSync(fullPath);
+                    if (stat.size === tracked.size && Math.floor(stat.mtimeMs) === Math.floor(tracked.modifiedAt)) {
+                        continue;
+                    }
                 }
                 catch (error) {
-                    (0, errors_1.logDebug)('Skipping unreadable file during sync', { filePath, error: String(error) });
+                    (0, errors_1.logDebug)('Skipping unstattable file during sync', { filePath, error: String(error) });
                     continue;
                 }
-                const contentHash = hashContent(content);
-                const tracked = this.queries.getFileByPath(filePath);
-                if (!tracked) {
-                    filesToIndex.push(filePath);
-                    changedFilePaths.push(filePath);
-                    filesAdded++;
-                }
-                else if (tracked.contentHash !== contentHash) {
-                    filesToIndex.push(filePath);
-                    changedFilePaths.push(filePath);
-                    filesModified++;
-                }
             }
-        }
-        else {
-            // === Fallback: full scan (non-git project or git failure) ===
-            const currentFiles = new Set(scanDirectory(this.rootDir));
-            filesChecked = currentFiles.size;
-            // Build Map for O(1) lookups instead of .find() per file
-            const trackedFiles = this.queries.getAllFiles();
-            const trackedMap = new Map();
-            for (const f of trackedFiles) {
-                trackedMap.set(f.path, f);
+            // New, or size/mtime changed — read + hash to confirm a real content change.
+            let content;
+            try {
+                content = fs.readFileSync(fullPath, 'utf-8');
             }
-            // Find files to remove (in DB but not on disk)
-            for (const tracked of trackedFiles) {
-                if (!currentFiles.has(tracked.path)) {
-                    this.queries.deleteFile(tracked.path);
-                    filesRemoved++;
-                }
+            catch (error) {
+                (0, errors_1.logDebug)('Skipping unreadable file during sync', { filePath, error: String(error) });
+                continue;
             }
-            // Find files to add or update
-            for (const filePath of currentFiles) {
-                const fullPath = path.join(this.rootDir, filePath);
-                let content;
-                try {
-                    content = fs.readFileSync(fullPath, 'utf-8');
-                }
-                catch (error) {
-                    (0, errors_1.logDebug)('Skipping unreadable file during sync', { filePath, error: String(error) });
-                    continue;
-                }
-                const contentHash = hashContent(content);
-                const tracked = trackedMap.get(filePath);
-                if (!tracked) {
-                    filesToIndex.push(filePath);
-                    changedFilePaths.push(filePath);
-                    filesAdded++;
-                }
-                else if (tracked.contentHash !== contentHash) {
-                    filesToIndex.push(filePath);
-                    changedFilePaths.push(filePath);
-                    filesModified++;
-                }
+            const contentHash = hashContent(content);
+            if (!tracked) {
+                filesToIndex.push(filePath);
+                changedFilePaths.push(filePath);
+                filesAdded++;
+            }
+            else if (tracked.contentHash !== contentHash) {
+                filesToIndex.push(filePath);
+                changedFilePaths.push(filePath);
+                filesModified++;
             }
         }
         // Load only grammars needed for changed files