@optave/codegraph 3.9.4 → 3.9.5

package/dist/domain/graph/builder/stages/collect-files.js

@@ -7,16 +7,18 @@
  */
 import fs from 'node:fs';
 import path from 'node:path';
+import { performance } from 'node:perf_hooks';
 import { debug, info } from '../../../../infrastructure/logger.js';
 import { normalizePath } from '../../../../shared/constants.js';
+import { compileGlobs } from '../../../../shared/globs.js';
 import { readJournal } from '../../journal.js';
-import { collectFiles as collectFilesUtil } from '../helpers.js';
+import { collectFiles as collectFilesUtil, passesIncludeExclude } from '../helpers.js';
 /**
  * Reconstruct allFiles from DB file_hashes + journal deltas.
  * Returns null when the fast path isn't applicable (first build, no journal, etc).
  */
 function tryFastCollect(ctx) {
-    const { db, rootDir } = ctx;
+    const { db, rootDir, config } = ctx;
     const useNative = ctx.engineName === 'native' && !!ctx.nativeDb?.getCollectFilesData;
     // 1. Check that file_hashes table exists and has entries
     let dbFileCount;
@@ -63,10 +65,20 @@ function tryFastCollect(ctx) {
             fileSet.add(changed);
         }
     }
-    // 5. Convert to absolute paths and compute directories
+    // 5. Convert to absolute paths and compute directories, honoring
+    //    config.include / config.exclude globs so incremental builds reflect
+    //    config changes (paths from the DB were collected under older config).
+    const includeRegexes = compileGlobs(config?.include);
+    const excludeRegexes = compileGlobs(config?.exclude);
+    const hasGlobFilters = includeRegexes.length > 0 || excludeRegexes.length > 0;
     const files = [];
     const directories = new Set();
     for (const relPath of fileSet) {
+        if (hasGlobFilters) {
+            const normRel = normalizePath(relPath);
+            if (!passesIncludeExclude(normRel, includeRegexes, excludeRegexes))
+                continue;
+        }
         const absPath = path.join(rootDir, relPath);
         files.push(absPath);
         directories.add(path.dirname(absPath));
@@ -77,42 +89,62 @@ function tryFastCollect(ctx) {
 export async function collectFiles(ctx) {
     const { rootDir, config, opts } = ctx;
     if (opts.scope) {
-        // Scoped rebuild: rebuild only specified files
+        // Scoped rebuild: rebuild only specified files.
+        //
+        // Timer only wraps the filesystem-walk portion (existence checks + file
+        // list construction). Change-detection outputs (parseChanges, removed,
+        // isFullBuild) are attributed to detectMs for semantic consistency with
+        // the non-scoped path, even though this stage computes them.
+        const start = performance.now();
         const scopedFiles = opts.scope.map((f) => normalizePath(f));
         const existing = [];
         const missing = [];
-        for (const rel of scopedFiles) {
-            const abs = path.join(rootDir, rel);
-            if (fs.existsSync(abs)) {
-                existing.push({ file: abs, relPath: rel });
-            }
-            else {
-                missing.push(rel);
+        try {
+            for (const rel of scopedFiles) {
+                const abs = path.join(rootDir, rel);
+                if (fs.existsSync(abs)) {
+                    existing.push({ file: abs, relPath: rel });
+                }
+                else {
+                    missing.push(rel);
+                }
             }
+            ctx.allFiles = existing.map((e) => e.file);
+            ctx.discoveredDirs = new Set(existing.map((e) => path.dirname(e.file)));
         }
-        ctx.allFiles = existing.map((e) => e.file);
-        ctx.discoveredDirs = new Set(existing.map((e) => path.dirname(e.file)));
+        finally {
+            ctx.timing.collectMs = performance.now() - start;
+        }
+        // Change-detection outputs — timed under detectMs for semantic parity.
+        const detectStart = performance.now();
         ctx.parseChanges = existing;
         ctx.metadataUpdates = [];
         ctx.removed = missing;
         ctx.isFullBuild = false;
+        ctx.timing.detectMs = (ctx.timing.detectMs ?? 0) + (performance.now() - detectStart);
         info(`Scoped rebuild: ${existing.length} files to rebuild, ${missing.length} to purge`);
         return;
     }
-    // Incremental fast path: reconstruct file list from DB + journal deltas
-    // instead of full recursive filesystem scan (~8ms savings on 473 files).
-    if (ctx.incremental && !ctx.forceFullRebuild) {
-        const fast = tryFastCollect(ctx);
-        if (fast) {
-            ctx.allFiles = fast.files;
-            ctx.discoveredDirs = fast.directories;
-            info(`Found ${ctx.allFiles.length} files (cached)`);
-            return;
+    const start = performance.now();
+    try {
+        // Incremental fast path: reconstruct file list from DB + journal deltas
+        // instead of full recursive filesystem scan (~8ms savings on 473 files).
+        if (ctx.incremental && !ctx.forceFullRebuild) {
+            const fast = tryFastCollect(ctx);
+            if (fast) {
+                ctx.allFiles = fast.files;
+                ctx.discoveredDirs = fast.directories;
+                info(`Found ${ctx.allFiles.length} files (cached)`);
+                return;
+            }
         }
+        const collected = collectFilesUtil(rootDir, [], config, new Set());
+        ctx.allFiles = collected.files;
+        ctx.discoveredDirs = collected.directories;
+        info(`Found ${ctx.allFiles.length} files to parse`);
+    }
+    finally {
+        ctx.timing.collectMs = performance.now() - start;
     }
-    const collected = collectFilesUtil(rootDir, [], config, new Set());
-    ctx.allFiles = collected.files;
-    ctx.discoveredDirs = collected.directories;
-    info(`Found ${ctx.allFiles.length} files to parse`);
 }
 //# sourceMappingURL=collect-files.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"collect-files.js","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/collect-files.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AACH,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,MAAM,sCAAsC,CAAC;AACnE,OAAO,EAAE,aAAa,EAAE,MAAM,iCAAiC,CAAC;AAChE,OAAO,EAAE,YAAY,EAAE,MAAM,6BAA6B,CAAC;AAC3D,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAE/C,OAAO,EAAE,YAAY,IAAI,gBAAgB,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AAEvF;;;GAGG;AACH,SAAS,cAAc,CACrB,GAAoB;IAEpB,MAAM,EAAE,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,GAAG,CAAC;IACpC,MAAM,SAAS,GAAG,GAAG,CAAC,UAAU,KAAK,QAAQ,IAAI,CAAC,CAAC,GAAG,CAAC,QAAQ,EAAE,mBAAmB,CAAC;IAErF,yDAAyD;IACzD,IAAI,WAAmB,CAAC;IACxB,IAAI,OAAiB,CAAC;IACtB,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,GAAG,GAAG,CAAC,QAAS,CAAC,mBAAoB,EAAE,CAAC;QAClD,WAAW,GAAG,IAAI,CAAC,KAAK,CAAC;QACzB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC;IACvB,CAAC;SAAM,CAAC;QACN,IAAI,CAAC;YACH,WAAW,GAAI,EAAE,CAAC,OAAO,CAAC,uCAAuC,CAAC,CAAC,GAAG,EAAoB,CAAC,CAAC,CAAC;QAC/F,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,IAAI,CAAC;QACd,CAAC;QACD,OAAO,GAAG,EAAE,CAAC,CAAC,yCAAyC;IACzD,CAAC;IACD,IAAI,WAAW,KAAK,CAAC;QAAE,OAAO,IAAI,CAAC;IAEnC,qEAAqE;IACrE,0EAA0E;IAC1E,kDAAkD;IAClD,MAAM,OAAO,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC;IACrC,IAAI,CAAC,OAAO,CAAC,KAAK;QAAE,OAAO,IAAI,CAAC;IAChC,MAAM,UAAU,GACd,CAAC,OAAO,CAAC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC;QAC/C,CAAC,OAAO,CAAC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;IAClD,IAAI,CAAC,UAAU;QAAE,OAAO,IAAI,CAAC;IAE7B,+DAA+D;IAC/D,IAAI,CAAC,SAAS,EAAE,CAAC;QACf,OAAO,GAAI,EAAE,CAAC,OAAO,CAAC,8BAA8B,CAAC,CAAC,GAAG,EAA8B,CAAC,GAAG,CACzF,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CACd,CAAC;IACJ,CAAC;IAED,uEAAuE;IACvE,MAAM,OAAO,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,CAAC;IACjC,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;QACpB,KAAK,MAAM,OAAO,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;YACtC,OAAO,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;QAC1B,CAAC;IACH,CAAC;IACD,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;QACpB,KAAK,MAAM,OAAO,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;YACtC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;QACvB,CAAC;IACH,CAAC;IAED,iEAAiE;IACjE,yEAAyE;IACzE,2EAA2E;IAC3E,MAAM,cAAc,GAAG,YAAY,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACrD,MAAM,cAAc,GAAG,YAAY,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACrD,MAAM,cAAc,GAAG,cAAc,CAAC,MAAM,GAAG,CAAC,IAAI,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC;IAE9E,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,MAAM,WAAW,GAAG,IAAI,GAAG,EAAU,CAAC;IACtC,KAAK,MAAM,OAAO,IAAI,OAAO,EAAE,CAAC;QAC9B,IAAI,cAAc,EAAE,CAAC;YACnB,MAAM,OAAO,GAAG,aAAa,CAAC,OAAO,CAAC,CAAC;YACvC,IAAI,CAAC,oBAAoB,CAAC,OAAO,EAAE,cAAc,EAAE,cAAc,CAAC;gBAAE,SAAS;QAC/E,CAAC;QACD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;QAC5C,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;QACpB,WAAW,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC;IACzC,CAAC;IAED,KAAK,CACH,2BAA2B,OAAO,CAAC,MAAM,uBAAuB,OAAO,CAAC,OAAO,EAAE,MAAM,IAAI,CAAC,KAAK,OAAO,CAAC,OAAO,EAAE,MAAM,IAAI,CAAC,MAAM,KAAK,CAAC,MAAM,QAAQ,CACxJ,CAAC;IACF,OAAO,EAAE,KAAK,EAAE,WAAW,EAAE,CAAC;AAChC,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,GAAoB;IACrD,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,GAAG,CAAC;IAEtC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC;QACf,gDAAgD;QAChD,EAAE;QACF,wEAAwE;QACxE,uEAAuE;QACvE,wEAAwE;QACxE,6DAA6D;QAC7D,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,EAAE,CAAC;QAChC,MAAM,WAAW,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAS,EAAE,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAC;QACpE,MAAM,QAAQ,GAA6C,EAAE,CAAC;QAC9D,MAAM,OAAO,GAAa,EAAE,CAAC;QAC7B,IAAI,CAAC;YACH,KAAK,MAAM,GAAG,IAAI,WAAW,EAAE,CAAC;gBAC9B,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;gBACpC,IAAI,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;oBACvB,QAAQ,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC,CAAC;gBAC7C,CAAC;qBAAM,CAAC;oBACN,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;gBACpB,CAAC;YACH,CAAC;YACD,GAAG,CAAC,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;YAC3C,GAAG,CAAC,cAAc,GAAG,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAC1E,CAAC;gBAAS,CAAC;YACT,GAAG,CAAC,MAAM,CAAC,SAAS,GAAG,WAAW,CAAC,GAAG,EAAE,GAAG,KAAK,CAAC;QACnD,CAAC;QACD,uEAAuE;QACvE,MAAM,WAAW,GAAG,WAAW,CAAC,GAAG,EAAE,CAAC;QACtC,GAAG,CAAC,YAAY,GAAG,QAAQ,CAAC;QAC5B,GAAG,CAAC,eAAe,GAAG,EAAE,CAAC;QACzB,GAAG,CAAC,OAAO,GAAG,OAAO,CAAC;QACtB,GAAG,CAAC,WAAW,GAAG,KAAK,CAAC;QACxB,GAAG,CAAC,MAAM,CAAC,QAAQ,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,QAAQ,IAAI,CAAC,CAAC,GAAG,CAAC,WAAW,CAAC,GAAG,EAAE,GAAG,WAAW,CAAC,CAAC;QACrF,IAAI,CAAC,mBAAmB,QAAQ,CAAC,MAAM,sBAAsB,OAAO,CAAC,MAAM,WAAW,CAAC,CAAC;QACxF,OAAO;IACT,CAAC;IAED,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,EAAE,CAAC;IAChC,IAAI,CAAC;QACH,wEAAwE;QACxE,yEAAyE;QACzE,IAAI,GAAG,CAAC,WAAW,IAAI,CAAC,GAAG,CAAC,gBAAgB,EAAE,CAAC;YAC7C,MAAM,IAAI,GAAG,cAAc,CAAC,GAAG,CAAC,CAAC;YACjC,IAAI,IAAI,EAAE,CAAC;gBACT,GAAG,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC;gBAC1B,GAAG,CAAC,cAAc,GAAG,IAAI,CAAC,WAAW,CAAC;gBACtC,IAAI,CAAC,SAAS,GAAG,CAAC,QAAQ,CAAC,MAAM,iBAAiB,CAAC,CAAC;gBACpD,OAAO;YACT,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAG,gBAAgB,CAAC,OAAO,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,GAAG,EAAU,CAAC,CAAC;QAC3E,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package/dist/domain/graph/builder/stages/detect-changes.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"detect-changes.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/detect-changes.ts"],"names":[],"mappings":"AAeA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAkfrD,wBAAsB,aAAa,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAwDvE"}
+{"version":3,"file":"detect-changes.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/detect-changes.ts"],"names":[],"mappings":"AAgBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAkfrD,wBAAsB,aAAa,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA+DvE"}

package/dist/domain/graph/builder/stages/detect-changes.js

@@ -7,6 +7,7 @@
  */
 import fs from 'node:fs';
 import path from 'node:path';
+import { performance } from 'node:perf_hooks';
 import { closeDb } from '../../../../db/index.js';
 import { debug, info } from '../../../../infrastructure/logger.js';
 import { normalizePath } from '../../../../shared/constants.js';
@@ -384,57 +385,65 @@ function handleIncrementalBuild(ctx) {
     purgeAndAddReverseDeps(ctx, changePaths, reverseDeps);
 }
 export async function detectChanges(ctx) {
-    const { db, allFiles, rootDir, incremental, forceFullRebuild, opts } = ctx;
-    if (opts.scope) {
-        handleScopedBuild(ctx);
-        return;
-    }
-    const increResult = incremental && !forceFullRebuild
-        ? getChangedFiles(db, allFiles, rootDir)
-        : {
-            changed: allFiles.map((f) => ({ file: f })),
-            removed: [],
-            isFullBuild: true,
-        };
-    ctx.removed = increResult.removed;
-    ctx.isFullBuild = increResult.isFullBuild;
-    ctx.parseChanges = increResult.changed
-        .filter((c) => !c.metadataOnly)
-        .map((c) => ({
-        file: c.file,
-        relPath: c.relPath,
-        content: c.content,
-        hash: c.hash,
-        stat: c.stat ? { mtime: Math.floor(c.stat.mtimeMs), size: c.stat.size } : undefined,
-        _reverseDepOnly: c._reverseDepOnly,
-    }));
-    ctx.metadataUpdates = increResult.changed
-        .filter((c) => !!c.metadataOnly && !!c.relPath && !!c.hash && !!c.stat)
-        .map((c) => ({
-        relPath: c.relPath,
-        hash: c.hash,
-        stat: { mtime: Math.floor(c.stat.mtimeMs), size: c.stat.size },
-    }));
-    if (!ctx.isFullBuild && ctx.parseChanges.length === 0 && ctx.removed.length === 0) {
-        const ranAnalysis = await runPendingAnalysis(ctx);
-        if (ranAnalysis) {
+    const start = performance.now();
+    try {
+        const { db, allFiles, rootDir, incremental, forceFullRebuild, opts } = ctx;
+        if (opts.scope) {
+            handleScopedBuild(ctx);
+            return;
+        }
+        const increResult = incremental && !forceFullRebuild
+            ? getChangedFiles(db, allFiles, rootDir)
+            : {
+                changed: allFiles.map((f) => ({ file: f })),
+                removed: [],
+                isFullBuild: true,
+            };
+        ctx.removed = increResult.removed;
+        ctx.isFullBuild = increResult.isFullBuild;
+        ctx.parseChanges = increResult.changed
+            .filter((c) => !c.metadataOnly)
+            .map((c) => ({
+            file: c.file,
+            relPath: c.relPath,
+            content: c.content,
+            hash: c.hash,
+            stat: c.stat ? { mtime: Math.floor(c.stat.mtimeMs), size: c.stat.size } : undefined,
+            _reverseDepOnly: c._reverseDepOnly,
+        }));
+        ctx.metadataUpdates = increResult.changed
+            .filter((c) => !!c.metadataOnly && !!c.relPath && !!c.hash && !!c.stat)
+            .map((c) => ({
+            relPath: c.relPath,
+            hash: c.hash,
+            stat: { mtime: Math.floor(c.stat.mtimeMs), size: c.stat.size },
+        }));
+        if (!ctx.isFullBuild && ctx.parseChanges.length === 0 && ctx.removed.length === 0) {
+            const ranAnalysis = await runPendingAnalysis(ctx);
+            if (ranAnalysis) {
+                closeDb(db);
+                writeJournalHeader(rootDir, Date.now());
+                ctx.earlyExit = true;
+                return;
+            }
+            healMetadata(ctx);
+            info('No changes detected. Graph is up to date.');
             closeDb(db);
             writeJournalHeader(rootDir, Date.now());
             ctx.earlyExit = true;
             return;
         }
-        healMetadata(ctx);
-        info('No changes detected. Graph is up to date.');
-        closeDb(db);
-        writeJournalHeader(rootDir, Date.now());
-        ctx.earlyExit = true;
-        return;
-    }
-    if (ctx.isFullBuild) {
-        handleFullBuild(ctx);
+        if (ctx.isFullBuild) {
+            handleFullBuild(ctx);
+        }
+        else {
+            handleIncrementalBuild(ctx);
+        }
     }
-    else {
-        handleIncrementalBuild(ctx);
+    finally {
+        // Additive to respect any partial detectMs contribution from collectFiles
+        // (scoped-rebuild path splits change-detection outputs across both stages).
+        ctx.timing.detectMs = (ctx.timing.detectMs ?? 0) + (performance.now() - start);
     }
 }
 //# sourceMappingURL=detect-changes.js.map

package/dist/domain/graph/builder/stages/detect-changes.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"finalize.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/finalize.ts"],"names":[],"mappings":"AAiBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAwMrD,wBAAsB,QAAQ,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA8ElE"}
+{"version":3,"file":"finalize.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/finalize.ts"],"names":[],"mappings":"AAkBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAuNrD,wBAAsB,QAAQ,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA8ElE"}

package/dist/domain/graph/builder/stages/finalize.js

@@ -3,6 +3,7 @@
  *
  * WASM cleanup, stats logging, drift detection, build metadata, registry, journal.
  */
+import fs from 'node:fs';
 import { tmpdir } from 'node:os';
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
@@ -68,6 +69,20 @@ function persistBuildMetadata(ctx, nodeCount, actualEdgeCount, buildNow) {
     // permanent mismatch whenever npm and crate versions diverge, forcing every
     // subsequent build to be a full rebuild.
     const codeVersionToWrite = ctx.engineName === 'native' && ctx.engineVersion ? ctx.engineVersion : CODEGRAPH_VERSION;
+    // Persist the repo root so downstream commands (e.g. `codegraph embed`)
+    // can resolve relative file paths regardless of the invoking cwd.
+    // Use realpathSync (symlink-resolving) to match the Rust engine's
+    // std::fs::canonicalize — otherwise the JS write here would overwrite the
+    // canonical path Rust wrote for native full builds and could re-introduce
+    // a non-canonical path when the project root is behind a symlink.
+    const resolvedRootDir = path.resolve(ctx.rootDir);
+    let rootDirToWrite = resolvedRootDir;
+    try {
+        rootDirToWrite = fs.realpathSync(resolvedRootDir);
+    }
+    catch {
+        /* realpath can fail (e.g. path no longer exists); fall back to resolve() */
+    }
     try {
         if (useNativeDb) {
             ctx.nativeDb.setBuildMeta(Object.entries({
@@ -78,6 +93,7 @@ function persistBuildMetadata(ctx, nodeCount, actualEdgeCount, buildNow) {
                 built_at: buildNow.toISOString(),
                 node_count: String(nodeCount),
                 edge_count: String(actualEdgeCount),
+                root_dir: rootDirToWrite,
             }).map(([key, value]) => ({ key, value: String(value) })));
         }
         else {
@@ -89,6 +105,7 @@ function persistBuildMetadata(ctx, nodeCount, actualEdgeCount, buildNow) {
                 built_at: buildNow.toISOString(),
                 node_count: nodeCount,
                 edge_count: actualEdgeCount,
+                root_dir: rootDirToWrite,
             });
         }
     }

package/dist/domain/graph/builder/stages/finalize.js.map

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

@@ -11,5 +11,20 @@ export declare function appendJournalEntries(rootDir: string, entries: Array<{
     deleted?: boolean;
 }>): void;
 export declare function writeJournalHeader(rootDir: string, timestamp: number): void;
+/**
+ * Atomically append entries while advancing the header timestamp.
+ *
+ * Used by the watcher: without this, the header timestamp stays frozen at the
+ * last build's finalize time while entries accumulate, so the next build's
+ * Tier 0 check sees `journal.timestamp < MAX(file_hashes.mtime)`, rejects the
+ * journal, and falls through to the expensive mtime+size / hash scan.
+ *
+ * Writes a tmp file then renames — a crash mid-rename leaves the previous
+ * journal state intact.
+ */
+export declare function appendJournalEntriesAndStampHeader(rootDir: string, entries: Array<{
+    file: string;
+    deleted?: boolean;
+}>, timestamp: number): void;
 export {};
 //# sourceMappingURL=journal.d.ts.map

package/dist/domain/graph/journal.d.ts.map

@@ -1 +1 @@
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