@optave/codegraph 3.9.4 → 3.9.5

package/README.md

@@ -617,18 +617,18 @@ Codegraph also extracts symbols from common callback patterns: Commander `.comma
 
 Self-measured on every release via CI ([build benchmarks](generated/benchmarks/BUILD-BENCHMARKS.md) | [embedding benchmarks](generated/benchmarks/EMBEDDING-BENCHMARKS.md) | [query benchmarks](generated/benchmarks/QUERY-BENCHMARKS.md) | [incremental benchmarks](generated/benchmarks/INCREMENTAL-BENCHMARKS.md) | [resolution precision/recall](tests/benchmarks/resolution/)):
 
-*Last updated: v3.9.3 (2026-04-13)*
+*Last updated: v3.9.4 (2026-04-18)*
 
 | Metric | Native | WASM |
 |---|---|---|
-| Build speed | **3.3 ms/file** | **15.9 ms/file** |
-| Query time | **30ms** | **42ms** |
-| No-op rebuild | **11ms** | **22ms** |
-| 1-file rebuild | **397ms** | **638ms** |
-| Query: fn-deps | **2.5ms** | **2.4ms** |
-| Query: path | **2.5ms** | **2.3ms** |
-| ~50,000 files (est.) | **~165.0s build** | **~795.0s build** |
-| Resolution precision | **90.7%** | — |
+| Build speed | **3.2 ms/file** | **16.3 ms/file** |
+| Query time | **29ms** | **44ms** |
+| No-op rebuild | **10ms** | **21ms** |
+| 1-file rebuild | **400ms** | **64ms** |
+| Query: fn-deps | **2.5ms** | **2.2ms** |
+| Query: path | **2.4ms** | **2.2ms** |
+| ~50,000 files (est.) | **~160.0s build** | **~815.0s build** |
+| Resolution precision | **90.3%** | — |
 | Resolution recall | **42.9%** | — |
 
 Metrics are normalized per file for cross-version comparability. Times above are for a full initial build — incremental rebuilds only re-parse changed files.
@@ -638,7 +638,7 @@ Metrics are normalized per file for cross-version comparability. Times above are
 | Language | Precision | Recall | TP | FP | FN | Edges | Dynamic |
 |----------|----------:|-------:|---:|---:|---:|------:|--------:|
 | javascript | 100.0% | 66.7% | 12 | 0 | 6 | 18 | 14/28 |
-| typescript | 100.0% | 75.0% | 15 | 0 | 5 | 20 | — |
+| typescript | 93.8% | 75.0% | 15 | 1 | 5 | 20 | — |
 | bash | 100.0% | 100.0% | 12 | 0 | 0 | 12 | 0/1 |
 | c | 100.0% | 100.0% | 9 | 0 | 0 | 9 | — |
 | clojure | 80.0% | 26.7% | 4 | 1 | 11 | 15 | — |

package/dist/cli/commands/watch.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"watch.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/watch.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAErD,eAAO,MAAM,OAAO,EAAE,iBAsBrB,CAAC"}
+{"version":3,"file":"watch.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/watch.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAErD,eAAO,MAAM,OAAO,EAAE,iBAwBrB,CAAC"}

package/dist/cli/commands/watch.js

@@ -4,6 +4,7 @@ export const command = {
     name: 'watch [dir]',
     description: 'Watch project for file changes and incrementally update the graph',
     options: [
+        ['-d, --db <path>', 'Path to graph.db'],
         ['--poll', 'Use stat-based polling (default on Windows to avoid ReFS/Dev Drive crashes)'],
         ['--native', 'Force native OS file watchers instead of polling'],
         ['--poll-interval <ms>', 'Polling interval in milliseconds (default: 2000)'],
@@ -20,6 +21,7 @@ export const command = {
             engine,
             poll,
             pollInterval: opts.pollInterval ? Number(opts.pollInterval) : undefined,
+            dbPath: opts.db ? path.resolve(opts.db) : undefined,
         });
     },
 };

package/dist/cli/commands/watch.js.map

@@ -1 +1 @@
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+{"version":3,"file":"watch.js","sourceRoot":"","sources":["../../../src/cli/commands/watch.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,YAAY,EAAE,MAAM,+BAA+B,CAAC;AAG7D,MAAM,CAAC,MAAM,OAAO,GAAsB;IACxC,IAAI,EAAE,aAAa;IACnB,WAAW,EAAE,mEAAmE;IAChF,OAAO,EAAE;QACP,CAAC,iBAAiB,EAAE,kBAAkB,CAAC;QACvC,CAAC,QAAQ,EAAE,6EAA6E,CAAC;QACzF,CAAC,UAAU,EAAE,kDAAkD,CAAC;QAChE,CAAC,sBAAsB,EAAE,kDAAkD,CAAC;KAC7E;IACD,KAAK,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,EAAE,IAAI,EAAE,GAAG;QAC5B,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC;QACzC,IAAI,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;YAC7B,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,4CAA4C,CAAC,CAAC;QAClE,CAAC;QACD,kFAAkF;QAClF,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAC;QAChE,MAAM,YAAY,CAAC,IAAI,EAAE;YACvB,MAAM;YACN,IAAI;YACJ,YAAY,EAAE,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,SAAS;YACvE,MAAM,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;SACpD,CAAC,CAAC;IACL,CAAC;CACF,CAAC"}

package/dist/cli.js

@@ -1,7 +1,29 @@
 #!/usr/bin/env node
 import { run } from './cli/index.js';
+import { disposeParsers } from './domain/parser.js';
 import { CodegraphError, toErrorMessage } from './shared/errors.js';
-run().catch((err) => {
+/**
+ * After the CLI command finishes, tear down any cached WASM parsers and the
+ * worker thread pool. The WASM parse worker (see `domain/wasm-worker-pool.ts`)
+ * keeps the event loop alive until `worker.terminate()` is called, so without
+ * this teardown short-lived commands like `codegraph build` would hang for
+ * minutes before Node gives up — surfacing in CI as `spawnSync ETIMEDOUT`
+ * even though the command's work is already complete.
+ *
+ * `disposeParsers` is safe to call when the pool was never instantiated
+ * (e.g. native engine, or commands that never parse): it no-ops cleanly.
+ */
+async function shutdown() {
+    try {
+        await disposeParsers();
+    }
+    catch {
+        /* don't mask the real exit status over a teardown failure */
+    }
+}
+run()
+    .then(shutdown)
+    .catch(async (err) => {
     if (err instanceof CodegraphError) {
         console.error(`codegraph [${err.code}]: ${err.message}`);
         if (err.file)
@@ -10,6 +32,7 @@ run().catch((err) => {
     else {
         console.error(`codegraph: fatal error — ${toErrorMessage(err)}`);
     }
+    await shutdown();
     process.exit(1);
 });
 //# sourceMappingURL=cli.js.map

package/dist/cli.js.map

@@ -1 +1 @@
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+{"version":3,"file":"cli.js","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AAEA,OAAO,EAAE,GAAG,EAAE,MAAM,gBAAgB,CAAC;AACrC,OAAO,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AACpD,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAEpE;;;;;;;;;;GAUG;AACH,KAAK,UAAU,QAAQ;IACrB,IAAI,CAAC;QACH,MAAM,cAAc,EAAE,CAAC;IACzB,CAAC;IAAC,MAAM,CAAC;QACP,6DAA6D;IAC/D,CAAC;AACH,CAAC;AAED,GAAG,EAAE;KACF,IAAI,CAAC,QAAQ,CAAC;KACd,KAAK,CAAC,KAAK,EAAE,GAAY,EAAE,EAAE;IAC5B,IAAI,GAAG,YAAY,cAAc,EAAE,CAAC;QAClC,OAAO,CAAC,KAAK,CAAC,cAAc,GAAG,CAAC,IAAI,MAAM,GAAG,CAAC,OAAO,EAAE,CAAC,CAAC;QACzD,IAAI,GAAG,CAAC,IAAI;YAAE,OAAO,CAAC,KAAK,CAAC,WAAW,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC;IACrD,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,KAAK,CAAC,4BAA4B,cAAc,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;IACnE,CAAC;IACD,MAAM,QAAQ,EAAE,CAAC;IACjB,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC,CAAC,CAAC"}

package/dist/domain/graph/builder/context.d.ts

@@ -57,6 +57,8 @@ export declare class PipelineContext {
     lineCountMap: Map<string, number>;
     timing: {
         setupMs?: number;
+        collectMs?: number;
+        detectMs?: number;
         parseMs?: number;
         insertMs?: number;
         resolveMs?: number;

package/dist/domain/graph/builder/context.d.ts.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/context.js.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/helpers.d.ts

@@ -1,14 +1,25 @@
 import type { BetterSqlite3Database, CodegraphConfig, PathAliases } from '../../../types.js';
 export declare const BUILTIN_RECEIVERS: Set<string>;
+/**
+ * Check whether a source file passes the configured include/exclude globs.
+ *
+ * Patterns are matched against the path relative to the project root,
+ * normalized to forward slashes (e.g. `src/foo/bar.ts`). When both lists
+ * are set, a file must match at least one include and no exclude.
+ */
+export declare function passesIncludeExclude(relPath: string, includeRegexes: readonly RegExp[], excludeRegexes: readonly RegExp[]): boolean;
 /**
  * Recursively collect all source files under `dir`.
  * When `directories` is a Set, also tracks which directories contain files.
+ *
+ * The first invocation establishes `dir` as the project root against which
+ * `config.include` / `config.exclude` globs are matched.
  */
-export declare function collectFiles(dir: string, files: string[], config: Partial<CodegraphConfig>, directories: Set<string>, _visited?: Set<string>): {
+export declare function collectFiles(dir: string, files: string[], config: Partial<CodegraphConfig>, directories: Set<string>, _visited?: Set<string>, _rootDir?: string, _includeRegexes?: readonly RegExp[], _excludeRegexes?: readonly RegExp[]): {
     files: string[];
     directories: Set<string>;
 };
-export declare function collectFiles(dir: string, files?: string[], config?: Partial<CodegraphConfig>, directories?: null, _visited?: Set<string>): string[];
+export declare function collectFiles(dir: string, files?: string[], config?: Partial<CodegraphConfig>, directories?: null, _visited?: Set<string>, _rootDir?: string, _includeRegexes?: readonly RegExp[], _excludeRegexes?: readonly RegExp[]): string[];
 /**
  * Load path aliases from tsconfig.json / jsconfig.json.
  */

package/dist/domain/graph/builder/helpers.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"helpers.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/helpers.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EACV,qBAAqB,EACrB,eAAe,EACf,WAAW,EAEZ,MAAM,mBAAmB,CAAC;AAE3B,eAAO,MAAM,iBAAiB,EAAE,GAAG,CAAC,MAAM,CA6BxC,CAAC;AAaH;;;;;;GAMG;AACH,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,MAAM,EACf,cAAc,EAAE,SAAS,MAAM,EAAE,EACjC,cAAc,EAAE,SAAS,MAAM,EAAE,GAChC,OAAO,CAIT;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAC1B,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,EAAE,EACf,MAAM,EAAE,OAAO,CAAC,eAAe,CAAC,EAChC,WAAW,EAAE,GAAG,CAAC,MAAM,CAAC,EACxB,QAAQ,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EACtB,QAAQ,CAAC,EAAE,MAAM,EACjB,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,EACnC,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,GAClC;IAAE,KAAK,EAAE,MAAM,EAAE,CAAC;IAAC,WAAW,EAAE,GAAG,CAAC,MAAM,CAAC,CAAA;CAAE,CAAC;AACjD,wBAAgB,YAAY,CAC1B,GAAG,EAAE,MAAM,EACX,KAAK,CAAC,EAAE,MAAM,EAAE,EAChB,MAAM,CAAC,EAAE,OAAO,CAAC,eAAe,CAAC,EACjC,WAAW,CAAC,EAAE,IAAI,EAClB,QAAQ,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EACtB,QAAQ,CAAC,EAAE,MAAM,EACjB,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,EACnC,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,GAClC,MAAM,EAAE,CAAC;AA+EZ;;GAEG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,MAAM,GAAG,WAAW,CA4B5D;AAED;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAEhD;AAED;;GAEG;AACH,wBAAgB,QAAQ,CAAC,QAAQ,EAAE,MAAM,GAAG;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAOnF;AAQD,wBAAgB,YAAY,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,GAAE,MAAU,GAAG,MAAM,CAa1E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,EAAE,EAAE,qBAAqB,EACzB,KAAK,EAAE,MAAM,EAAE,EACf,OAAO,GAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAM,GACpC,IAAI,CAGN;AA6CD;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,qBAAqB,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,GAAG,IAAI,CAanF;AAED;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,qBAAqB,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,GAAG,IAAI,CAanF"}

package/dist/domain/graph/builder/helpers.js

@@ -8,7 +8,8 @@ import fs from 'node:fs';
 import path from 'node:path';
 import { purgeFilesData } from '../../../db/index.js';
 import { warn } from '../../../infrastructure/logger.js';
-import { EXTENSIONS, IGNORE_DIRS } from '../../../shared/constants.js';
+import { EXTENSIONS, IGNORE_DIRS, normalizePath } from '../../../shared/constants.js';
+import { compileGlobs, matchesAny } from '../../../shared/globs.js';
 export const BUILTIN_RECEIVERS = new Set([
     'console',
     'Math',
@@ -53,9 +54,29 @@ function shouldSkipEntry(entry, extraIgnore) {
         return true;
     return false;
 }
-export function collectFiles(dir, files = [], config = {}, directories = null, _visited = new Set()) {
+/**
+ * Check whether a source file passes the configured include/exclude globs.
+ *
+ * Patterns are matched against the path relative to the project root,
+ * normalized to forward slashes (e.g. `src/foo/bar.ts`). When both lists
+ * are set, a file must match at least one include and no exclude.
+ */
+export function passesIncludeExclude(relPath, includeRegexes, excludeRegexes) {
+    if (includeRegexes.length > 0 && !matchesAny(includeRegexes, relPath))
+        return false;
+    if (excludeRegexes.length > 0 && matchesAny(excludeRegexes, relPath))
+        return false;
+    return true;
+}
+export function collectFiles(dir, files = [], config = {}, directories = null, _visited = new Set(), _rootDir, _includeRegexes, _excludeRegexes) {
     const trackDirs = directories instanceof Set;
     let hasFiles = false;
+    // First call: compute root and compile include/exclude patterns once,
+    // then pass them down recursive calls so we don't recompile per directory.
+    const rootDir = _rootDir ?? dir;
+    const includeRegexes = _includeRegexes ?? compileGlobs(config.include);
+    const excludeRegexes = _excludeRegexes ?? compileGlobs(config.exclude);
+    const hasGlobFilters = includeRegexes.length > 0 || excludeRegexes.length > 0;
     // Merge config ignoreDirs with defaults
     const extraIgnore = config.ignoreDirs ? new Set(config.ignoreDirs) : null;
     // Detect symlink loops (before I/O to avoid wasted readdirSync)
@@ -85,13 +106,18 @@ export function collectFiles(dir, files = [], config = {}, directories = null, _
         const full = path.join(dir, entry.name);
         if (entry.isDirectory()) {
             if (trackDirs) {
-                collectFiles(full, files, config, directories, _visited);
+                collectFiles(full, files, config, directories, _visited, rootDir, includeRegexes, excludeRegexes);
             }
             else {
-                collectFiles(full, files, config, null, _visited);
+                collectFiles(full, files, config, null, _visited, rootDir, includeRegexes, excludeRegexes);
             }
         }
         else if (EXTENSIONS.has(path.extname(entry.name))) {
+            if (hasGlobFilters) {
+                const rel = normalizePath(path.relative(rootDir, full));
+                if (!passesIncludeExclude(rel, includeRegexes, excludeRegexes))
+                    continue;
+            }
             files.push(full);
             hasFiles = true;
         }

package/dist/domain/graph/builder/helpers.js.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/pipeline.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pipeline.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/pipeline.ts"],"names":[],"mappings":"AAyBA,OAAO,KAAK,EAEV,cAAc,EACd,WAAW,EAGZ,MAAM,mBAAmB,CAAC;AA0wB3B;;;;GAIG;AACH,wBAAsB,UAAU,CAC9B,OAAO,EAAE,MAAM,EACf,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,WAAW,GAAG,SAAS,CAAC,CA8DlC"}
+{"version":3,"file":"pipeline.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/pipeline.ts"],"names":[],"mappings":"AA0BA,OAAO,KAAK,EAEV,cAAc,EACd,WAAW,EAIZ,MAAM,mBAAmB,CAAC;AA+4B3B;;;;GAIG;AACH,wBAAsB,UAAU,CAC9B,OAAO,EAAE,MAAM,EACf,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,WAAW,GAAG,SAAS,CAAC,CAkElC"}

package/dist/domain/graph/builder/pipeline.js

@@ -12,12 +12,13 @@ import { detectWorkspaces, loadConfig } from '../../../infrastructure/config.js'
 import { debug, info, warn } from '../../../infrastructure/logger.js';
 import { loadNative } from '../../../infrastructure/native.js';
 import { semverCompare } from '../../../infrastructure/update-check.js';
+import { normalizePath } from '../../../shared/constants.js';
 import { toErrorMessage } from '../../../shared/errors.js';
 import { CODEGRAPH_VERSION } from '../../../shared/version.js';
-import { getActiveEngine } from '../../parser.js';
+import { getActiveEngine, getInstalledWasmExtensions, parseFilesAuto } from '../../parser.js';
 import { setWorkspaces } from '../resolve.js';
 import { PipelineContext } from './context.js';
-import { loadPathAliases } from './helpers.js';
+import { batchInsertNodes, collectFiles as collectFilesUtil, loadPathAliases } from './helpers.js';
 import { NativeDbProxy } from './native-db-proxy.js';
 import { buildEdges } from './stages/build-edges.js';
 import { buildStructure } from './stages/build-structure.js';
@@ -78,6 +79,21 @@ function checkEngineSchemaMismatch(ctx) {
         ctx.forceFullRebuild = true;
     }
 }
+function warnOnEmbeddingsWipe(ctx) {
+    const willBeFullBuild = !ctx.incremental || ctx.forceFullRebuild;
+    if (!willBeFullBuild)
+        return;
+    let count = 0;
+    try {
+        count = ctx.db.prepare('SELECT COUNT(*) AS c FROM embeddings').get().c;
+    }
+    catch {
+        return; // embeddings table missing — nothing to warn about
+    }
+    if (count === 0)
+        return;
+    warn(`Full rebuild will discard ${count} embedding${count === 1 ? '' : 's'}; re-run \`codegraph embed\` after the build.`);
+}
 function loadAliases(ctx) {
     ctx.aliases = loadPathAliases(ctx.rootDir);
     if (ctx.config.aliases) {
@@ -117,6 +133,7 @@ function setupPipeline(ctx) {
         ctx.opts.incremental !== false && ctx.config.build && ctx.config.build.incremental !== false;
     initializeEngine(ctx);
     checkEngineSchemaMismatch(ctx);
+    warnOnEmbeddingsWipe(ctx);
     loadAliases(ctx);
     // Workspace packages (monorepo)
     const workspaces = detectWorkspaces(ctx.rootDir);
@@ -131,6 +148,8 @@ function formatTimingResult(ctx) {
     return {
         phases: {
             setupMs: +(t.setupMs ?? 0).toFixed(1),
+            collectMs: +(t.collectMs ?? 0).toFixed(1),
+            detectMs: +(t.detectMs ?? 0).toFixed(1),
             parseMs: +(t.parseMs ?? 0).toFixed(1),
             insertMs: +(t.insertMs ?? 0).toFixed(1),
             resolveMs: +(t.resolveMs ?? 0).toFixed(1),
@@ -422,7 +441,9 @@ async function runPostNativeAnalysis(ctx, allFileSymbols, changedFiles) {
 function formatNativeTimingResult(p, structurePatchMs, analysisTiming) {
     return {
         phases: {
-            setupMs: +((p.setupMs ?? 0) + (p.collectMs ?? 0) + (p.detectMs ?? 0)).toFixed(1),
+            setupMs: +(p.setupMs ?? 0).toFixed(1),
+            collectMs: +(p.collectMs ?? 0).toFixed(1),
+            detectMs: +(p.detectMs ?? 0).toFixed(1),
             parseMs: +(p.parseMs ?? 0).toFixed(1),
             insertMs: +(p.insertMs ?? 0).toFixed(1),
             resolveMs: +(p.resolveMs ?? 0).toFixed(1),
@@ -552,9 +573,110 @@ async function tryNativeOrchestrator(ctx) {
             analysisTiming = await runPostNativeAnalysis(ctx, fileSymbols, result.changedFiles);
         }
     }
+    // Engine parity: the native orchestrator silently drops files whose
+    // Rust extractor/grammar is missing or fails (e.g. HCL, Scala, Swift on
+    // stale native binaries). WASM handles those — backfill via WASM so both
+    // engines process the same file set (#967).
+    //
+    // Only runs on full builds: incremental builds only touch changed files,
+    // which are parsed through parseFilesAuto (which has its own per-file
+    // backfill), so a full filesystem scan here would be wasted work.
+    if (result.isFullBuild) {
+        await backfillNativeDroppedFiles(ctx);
+    }
     closeDbPair({ db: ctx.db, nativeDb: ctx.nativeDb });
     return formatNativeTimingResult(p, structurePatchMs, analysisTiming);
 }
+/**
+ * Backfill files that the native orchestrator silently dropped during parse.
+ * Falls back to WASM + inserts file/symbol nodes so engine counts match (#967).
+ */
+async function backfillNativeDroppedFiles(ctx) {
+    // Needs a real better-sqlite3 connection for INSERT.
+    if (ctx.nativeFirstProxy) {
+        closeNativeDb(ctx, 'pre-parity-backfill');
+        ctx.db = openDb(ctx.dbPath);
+        ctx.nativeFirstProxy = false;
+    }
+    const collected = collectFilesUtil(ctx.rootDir, [], ctx.config, new Set());
+    const expected = new Set(collected.files.map((f) => normalizePath(path.relative(ctx.rootDir, f))));
+    const existingRows = ctx.db
+        .prepare("SELECT DISTINCT file FROM nodes WHERE kind = 'file'")
+        .all();
+    const existing = new Set(existingRows.map((r) => r.file));
+    // Restrict backfill to files with an installed WASM grammar. Extensions in
+    // LANGUAGE_REGISTRY without a shipped grammar file (e.g. groovy, erlang on
+    // minimal installs) can't be parsed by either engine, so they're not a
+    // native regression — excluding them keeps the warn count meaningful.
+    const installedExts = getInstalledWasmExtensions();
+    const missingAbs = [];
+    for (const rel of expected) {
+        if (existing.has(rel))
+            continue;
+        const ext = path.extname(rel).toLowerCase();
+        if (!installedExts.has(ext))
+            continue;
+        missingAbs.push(path.join(ctx.rootDir, rel));
+    }
+    if (missingAbs.length === 0)
+        return;
+    warn(`Native orchestrator dropped ${missingAbs.length} file(s); backfilling via WASM for engine parity`);
+    const wasmResults = await parseFilesAuto(missingAbs, ctx.rootDir, { engine: 'wasm' });
+    const rows = [];
+    const exportKeys = [];
+    for (const [relPath, symbols] of wasmResults) {
+        // File row — mirrors insertDefinitionsAndExports: qualified_name is null.
+        rows.push([relPath, 'file', relPath, 0, null, null, null, null, null]);
+        for (const def of symbols.definitions ?? []) {
+            // Populate qualified_name/scope the same way the JS fallback does so
+            // downstream queries (cross-file references, "go to definition") find
+            // these symbols.
+            const dotIdx = def.name.lastIndexOf('.');
+            const scope = dotIdx !== -1 ? def.name.slice(0, dotIdx) : null;
+            rows.push([
+                def.name,
+                def.kind,
+                relPath,
+                def.line,
+                def.endLine ?? null,
+                null,
+                def.name,
+                scope,
+                def.visibility ?? null,
+            ]);
+        }
+        // Exports: insert the row (INSERT OR IGNORE — a matching definition row
+        // is a no-op) and queue a key for the second-pass exported=1 update, so
+        // queries filtering on exported=1 find backfilled symbols (#970).
+        for (const exp of symbols.exports ?? []) {
+            rows.push([exp.name, exp.kind, relPath, exp.line, null, null, exp.name, null, null]);
+            exportKeys.push([exp.name, exp.kind, relPath, exp.line]);
+        }
+    }
+    const db = ctx.db;
+    batchInsertNodes(db, rows);
+    // Mark exported symbols in batches — mirrors insertDefinitionsAndExports.
+    if (exportKeys.length > 0) {
+        const EXPORT_CHUNK = 500;
+        const exportStmtCache = new Map();
+        for (let i = 0; i < exportKeys.length; i += EXPORT_CHUNK) {
+            const end = Math.min(i + EXPORT_CHUNK, exportKeys.length);
+            const chunkSize = end - i;
+            let updateStmt = exportStmtCache.get(chunkSize);
+            if (!updateStmt) {
+                const conditions = Array.from({ length: chunkSize }, () => '(name = ? AND kind = ? AND file = ? AND line = ?)').join(' OR ');
+                updateStmt = db.prepare(`UPDATE nodes SET exported = 1 WHERE ${conditions}`);
+                exportStmtCache.set(chunkSize, updateStmt);
+            }
+            const vals = [];
+            for (let j = i; j < end; j++) {
+                const k = exportKeys[j];
+                vals.push(k[0], k[1], k[2], k[3]);
+            }
+            updateStmt.run(...vals);
+        }
+    }
+}
 // ── Pipeline stages execution ───────────────────────────────────────────
 async function runPipelineStages(ctx) {
     // ── WASM / fallback dual-connection mode ─────────────────────────────
@@ -683,6 +805,10 @@ export async function buildGraph(rootDir, opts = {}) {
                 if (prevVersion && prevVersion !== CODEGRAPH_VERSION) {
                     info(`Codegraph version changed (${prevVersion} → ${CODEGRAPH_VERSION}), promoting to full rebuild.`);
                     ctx.forceFullRebuild = true;
+                    // Re-check embeddings: the initial warnOnEmbeddingsWipe ran before
+                    // forceFullRebuild was set here, so the silent-data-loss guard
+                    // would otherwise miss this late-promotion path (#986 follow-up).
+                    warnOnEmbeddingsWipe(ctx);
                 }
             }
         }

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package/dist/domain/graph/builder/stages/collect-files.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"collect-files.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/collect-files.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA2ErD,wBAAsB,YAAY,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA0CtE"}
+{"version":3,"file":"collect-files.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/collect-files.ts"],"names":[],"mappings":"AAcA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAqFrD,wBAAsB,YAAY,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA4DtE"}