@optave/codegraph 3.5.0 → 3.7.0

package/dist/domain/graph/builder/stages/build-structure.js

@@ -5,8 +5,8 @@
  */
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { debug } from '#infrastructure/logger.js';
-import { normalizePath } from '#shared/constants.js';
+import { debug } from '../../../../infrastructure/logger.js';
+import { normalizePath } from '../../../../shared/constants.js';
 import { readFileSafe } from '../helpers.js';
 export async function buildStructure(ctx) {
     const { db, fileSymbols, rootDir, discoveredDirs, allSymbols, isFullBuild } = ctx;
@@ -34,8 +34,9 @@ export async function buildStructure(ctx) {
     // loading ALL definitions from DB (~8ms) and recomputing ALL metrics (~15ms).
     // Gate: ≤5 changed files AND significantly more existing files (>20) to
     // avoid triggering on small test fixtures where directory metrics matter.
+    const useNativeReads = ctx.engineName === 'native' && !!ctx.nativeDb;
     const existingFileCount = !isFullBuild
-        ? (ctx.nativeDb
+        ? (useNativeReads
             ? ctx.nativeDb.queryGet("SELECT COUNT(*) as c FROM nodes WHERE kind = 'file'", [])
             : db.prepare("SELECT COUNT(*) as c FROM nodes WHERE kind = 'file'").get()).c
         : 0;
@@ -73,7 +74,8 @@ export async function buildStructure(ctx) {
         let roleSummary = null;
         // Use NativeDatabase persistent connection (Phase 6.15+).
         // Standalone napi functions were removed in 6.17 — falls through to JS if nativeDb unavailable.
-        if (ctx.nativeDb?.classifyRolesFull) {
+        // Note: classifyRoles* both read (fan-in/fan-out) and write (UPDATE nodes SET role).
+        if (useNativeReads && ctx.nativeDb?.classifyRolesFull) {
             const nativeResult = changedFileList && changedFileList.length > 0
                 ? ctx.nativeDb.classifyRolesIncremental(changedFileList)
                 : ctx.nativeDb.classifyRolesFull();
@@ -96,7 +98,7 @@ export async function buildStructure(ctx) {
         // Fall back to JS path
         if (!roleSummary) {
             const { classifyNodeRoles } = (await import('../../../../features/structure.js'));
-            roleSummary = classifyNodeRoles(db, changedFileList);
+            roleSummary = classifyNodeRoles(ctx.db, changedFileList);
         }
         debug(`Roles${changedFileList ? ` (incremental, ${changedFileList.length} files)` : ''}: ${Object.entries(roleSummary)
             .map(([r, c]) => `${r}=${c}`)

package/dist/domain/graph/builder/stages/build-structure.js.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/stages/collect-files.js

@@ -7,8 +7,8 @@
  */
 import fs from 'node:fs';
 import path from 'node:path';
-import { debug, info } from '#infrastructure/logger.js';
-import { normalizePath } from '#shared/constants.js';
+import { debug, info } from '../../../../infrastructure/logger.js';
+import { normalizePath } from '../../../../shared/constants.js';
 import { readJournal } from '../../journal.js';
 import { collectFiles as collectFilesUtil } from '../helpers.js';
 /**

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,KAAK,EAAE,IAAI,EAAE,MAAM,sCAAsC,CAAC;AACnE,OAAO,EAAE,aAAa,EAAE,MAAM,iCAAiC,CAAC;AAChE,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAE/C,OAAO,EAAE,YAAY,IAAI,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjE;;;GAGG;AACH,SAAS,cAAc,CACrB,GAAoB;IAEpB,MAAM,EAAE,EAAE,EAAE,OAAO,EAAE,GAAG,GAAG,CAAC;IAE5B,yDAAyD;IACzD,IAAI,WAAmB,CAAC;IACxB,IAAI,CAAC;QACH,WAAW,GAAI,EAAE,CAAC,OAAO,CAAC,uCAAuC,CAAC,CAAC,GAAG,EAAoB,CAAC,CAAC,CAAC;IAC/F,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,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,MAAM,OAAO,GAAI,EAAE,CAAC,OAAO,CAAC,8BAA8B,CAAC,CAAC,GAAG,EAA8B,CAAC,GAAG,CAC/F,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CACd,CAAC;IAEF,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,uDAAuD;IACvD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,MAAM,WAAW,GAAG,IAAI,GAAG,EAAU,CAAC;IACtC,KAAK,MAAM,OAAO,IAAI,OAAO,EAAE,CAAC;QAC9B,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,+CAA+C;QAC/C,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,KAAK,MAAM,GAAG,IAAI,WAAW,EAAE,CAAC;YAC9B,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;YACpC,IAAI,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;gBACvB,QAAQ,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC,CAAC;YAC7C,CAAC;iBAAM,CAAC;gBACN,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YACpB,CAAC;QACH,CAAC;QACD,GAAG,CAAC,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;QAC3C,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;QACxE,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,IAAI,CAAC,mBAAmB,QAAQ,CAAC,MAAM,sBAAsB,OAAO,CAAC,MAAM,WAAW,CAAC,CAAC;QACxF,OAAO;IACT,CAAC;IAED,wEAAwE;IACxE,yEAAyE;IACzE,IAAI,GAAG,CAAC,WAAW,IAAI,CAAC,GAAG,CAAC,gBAAgB,EAAE,CAAC;QAC7C,MAAM,IAAI,GAAG,cAAc,CAAC,GAAG,CAAC,CAAC;QACjC,IAAI,IAAI,EAAE,CAAC;YACT,GAAG,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC;YAC1B,GAAG,CAAC,cAAc,GAAG,IAAI,CAAC,WAAW,CAAC;YACtC,IAAI,CAAC,SAAS,GAAG,CAAC,QAAQ,CAAC,MAAM,iBAAiB,CAAC,CAAC;YACpD,OAAO;QACT,CAAC;IACH,CAAC;IAED,MAAM,SAAS,GAAG,gBAAgB,CAAC,OAAO,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,GAAG,EAAU,CAAC,CAAC;IAC3E,GAAG,CAAC,QAAQ,GAAG,SAAS,CAAC,KAAK,CAAC;IAC/B,GAAG,CAAC,cAAc,GAAG,SAAS,CAAC,WAAW,CAAC;IAC3C,IAAI,CAAC,SAAS,GAAG,CAAC,QAAQ,CAAC,MAAM,iBAAiB,CAAC,CAAC;AACtD,CAAC"}

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;AA4ZrD,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":"AAeA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA4ZrD,wBAAsB,aAAa,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA6DvE"}

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

@@ -244,7 +244,7 @@ function purgeAndAddReverseDeps(ctx, changePaths, reverseDeps) {
     if (hasPurge || hasReverseDeps) {
         const filesToPurge = hasPurge ? [...ctx.removed, ...changePaths] : [];
         // Prefer NativeDatabase: purge + reverse-dep edge deletion in one transaction (#670)
-        if (ctx.nativeDb?.purgeFilesData) {
+        if (ctx.engineName === 'native' && ctx.nativeDb?.purgeFilesData) {
             ctx.nativeDb.purgeFilesData(filesToPurge, false, hasReverseDeps ? reverseDepList : undefined);
         }
         else {
@@ -323,7 +323,7 @@ export async function detectChanges(ctx) {
         return;
     }
     const increResult = incremental && !forceFullRebuild
-        ? getChangedFiles(db, allFiles, rootDir, ctx.nativeDb)
+        ? getChangedFiles(db, allFiles, rootDir, ctx.engineName === 'native' ? ctx.nativeDb : undefined)
         : {
             changed: allFiles.map((f) => ({ file: f })),
             removed: [],

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;AAErD,wBAAsB,QAAQ,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA6MlE"}
+{"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;AA2KrD,wBAAsB,QAAQ,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAsElE"}

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

@@ -10,10 +10,8 @@ import { closeDbPair, closeDbPairDeferred, getBuildMeta, setBuildMeta, } from '.
 import { debug, info, warn } from '../../../../infrastructure/logger.js';
 import { CODEGRAPH_VERSION } from '../../../../shared/version.js';
 import { writeJournalHeader } from '../../journal.js';
-export async function finalize(ctx) {
-    const { db, allSymbols, rootDir, isFullBuild, hasEmbeddings, config, opts, schemaVersion } = ctx;
-    const t0 = performance.now();
-    // Release cached WASM trees
+/** Release cached WASM parse trees to free memory. */
+function releaseWasmTrees(allSymbols) {
     for (const [, symbols] of allSymbols) {
         const tree = symbols._tree;
         if (tree && typeof tree.delete === 'function') {
@@ -27,110 +25,109 @@ export async function finalize(ctx) {
         symbols._tree = undefined;
         symbols._langId = undefined;
     }
-    // Capture a single wall-clock timestamp for the current build — used for
-    // both the stale-embeddings comparison and the persisted built_at metadata.
-    const buildNow = new Date();
-    const nodeCount = db.prepare('SELECT COUNT(*) as c FROM nodes').get().c;
-    const actualEdgeCount = db.prepare('SELECT COUNT(*) as c FROM edges').get().c;
-    info(`Graph built: ${nodeCount} nodes, ${actualEdgeCount} edges`);
-    info(`Stored in ${ctx.dbPath}`);
-    // Incremental drift detection — skip for small incremental changes where
-    // count fluctuation is expected (reverse-dep edge churn).
-    if (!isFullBuild && allSymbols.size > 3) {
-        const prevNodes = ctx.nativeDb
-            ? ctx.nativeDb.getBuildMeta('node_count')
-            : getBuildMeta(db, 'node_count');
-        const prevEdges = ctx.nativeDb
-            ? ctx.nativeDb.getBuildMeta('edge_count')
-            : getBuildMeta(db, 'edge_count');
-        if (prevNodes && prevEdges) {
-            const prevN = Number(prevNodes);
-            const prevE = Number(prevEdges);
-            if (prevN > 0) {
-                const nodeDrift = Math.abs(nodeCount - prevN) / prevN;
-                const edgeDrift = prevE > 0 ? Math.abs(actualEdgeCount - prevE) / prevE : 0;
-                const driftThreshold = config.build?.driftThreshold ?? 0.2;
-                if (nodeDrift > driftThreshold || edgeDrift > driftThreshold) {
-                    warn(`Incremental build diverged significantly from previous counts (nodes: ${prevN}\u2192${nodeCount} [${(nodeDrift * 100).toFixed(1)}%], edges: ${prevE}\u2192${actualEdgeCount} [${(edgeDrift * 100).toFixed(1)}%], threshold: ${(driftThreshold * 100).toFixed(0)}%). Consider rebuilding with --no-incremental.`);
-                }
-            }
+}
+/**
+ * Detect significant drift between current and previous node/edge counts.
+ * Skipped for small incremental changes where count fluctuation is expected.
+ */
+function detectIncrementalDrift(ctx, nodeCount, actualEdgeCount) {
+    const { db, allSymbols, config } = ctx;
+    const useNativeDb = ctx.engineName === 'native' && !!ctx.nativeDb;
+    if (ctx.isFullBuild || allSymbols.size <= 3)
+        return;
+    const prevNodes = useNativeDb
+        ? ctx.nativeDb.getBuildMeta('node_count')
+        : getBuildMeta(db, 'node_count');
+    const prevEdges = useNativeDb
+        ? ctx.nativeDb.getBuildMeta('edge_count')
+        : getBuildMeta(db, 'edge_count');
+    if (!prevNodes || !prevEdges)
+        return;
+    const prevN = Number(prevNodes);
+    const prevE = Number(prevEdges);
+    if (prevN <= 0)
+        return;
+    const nodeDrift = Math.abs(nodeCount - prevN) / prevN;
+    const edgeDrift = prevE > 0 ? Math.abs(actualEdgeCount - prevE) / prevE : 0;
+    const driftThreshold = config.build?.driftThreshold ?? 0.2;
+    if (nodeDrift > driftThreshold || edgeDrift > driftThreshold) {
+        warn(`Incremental build diverged significantly from previous counts (nodes: ${prevN}\u2192${nodeCount} [${(nodeDrift * 100).toFixed(1)}%], edges: ${prevE}\u2192${actualEdgeCount} [${(edgeDrift * 100).toFixed(1)}%], threshold: ${(driftThreshold * 100).toFixed(0)}%). Consider rebuilding with --no-incremental.`);
+    }
+}
+/**
+ * Persist build metadata (engine, version, counts, timestamp).
+ * Skipped for small incremental builds to avoid WAL fsync cost.
+ */
+function persistBuildMetadata(ctx, nodeCount, actualEdgeCount, buildNow) {
+    const useNativeDb = ctx.engineName === 'native' && !!ctx.nativeDb;
+    if (!ctx.isFullBuild && ctx.allSymbols.size <= 3)
+        return;
+    try {
+        if (useNativeDb) {
+            ctx.nativeDb.setBuildMeta(Object.entries({
+                engine: ctx.engineName,
+                engine_version: ctx.engineVersion || '',
+                codegraph_version: CODEGRAPH_VERSION,
+                schema_version: String(ctx.schemaVersion),
+                built_at: buildNow.toISOString(),
+                node_count: String(nodeCount),
+                edge_count: String(actualEdgeCount),
+            }).map(([key, value]) => ({ key, value: String(value) })));
+        }
+        else {
+            setBuildMeta(ctx.db, {
+                engine: ctx.engineName,
+                engine_version: ctx.engineVersion || '',
+                codegraph_version: CODEGRAPH_VERSION,
+                schema_version: String(ctx.schemaVersion),
+                built_at: buildNow.toISOString(),
+                node_count: nodeCount,
+                edge_count: actualEdgeCount,
+            });
         }
     }
-    // For small incremental builds, skip persisting build metadata — the
-    // engine/version/schema haven't changed (would have triggered a full rebuild),
-    // built_at is only used by stale-embeddings check (skipped for incremental),
-    // and counts are only used by drift detection (skipped for ≤3 files).
-    // This avoids a transaction commit + WAL fsync (~15-30ms).
-    // Threshold aligned with drift detection gate (allSymbols.size > 3) so stored
-    // counts stay fresh whenever drift detection reads them.
-    if (isFullBuild || allSymbols.size > 3) {
+    catch (err) {
+        warn(`Failed to write build metadata: ${err.message}`);
+    }
+}
+/**
+ * Run advisory checks on full builds: orphaned embeddings, stale embeddings,
+ * and unused exports. Informational only — does not affect correctness.
+ */
+function runAdvisoryChecks(db, hasEmbeddings, buildNow) {
+    // Orphaned embeddings warning
+    if (hasEmbeddings) {
         try {
-            if (ctx.nativeDb) {
-                ctx.nativeDb.setBuildMeta(Object.entries({
-                    engine: ctx.engineName,
-                    engine_version: ctx.engineVersion || '',
-                    codegraph_version: CODEGRAPH_VERSION,
-                    schema_version: String(schemaVersion),
-                    built_at: buildNow.toISOString(),
-                    node_count: String(nodeCount),
-                    edge_count: String(actualEdgeCount),
-                }).map(([key, value]) => ({ key, value: String(value) })));
-            }
-            else {
-                setBuildMeta(db, {
-                    engine: ctx.engineName,
-                    engine_version: ctx.engineVersion || '',
-                    codegraph_version: CODEGRAPH_VERSION,
-                    schema_version: String(schemaVersion),
-                    built_at: buildNow.toISOString(),
-                    node_count: nodeCount,
-                    edge_count: actualEdgeCount,
-                });
+            const orphaned = db
+                .prepare('SELECT COUNT(*) as c FROM embeddings WHERE node_id NOT IN (SELECT id FROM nodes)')
+                .get().c;
+            if (orphaned > 0) {
+                warn(`${orphaned} embeddings are orphaned (nodes changed). Run "codegraph embed" to refresh.`);
             }
         }
-        catch (err) {
-            warn(`Failed to write build metadata: ${err.message}`);
+        catch {
+            /* ignore - embeddings table may have been dropped */
         }
     }
-    // Skip expensive advisory queries for incremental builds — these are
-    // informational warnings that don't affect correctness and cost ~40-60ms.
-    if (!isFullBuild) {
-        debug('Finalize: skipping advisory queries (orphaned/stale embeddings, unused exports) for incremental build');
-    }
-    else {
-        // Orphaned embeddings warning
-        if (hasEmbeddings) {
-            try {
-                const orphaned = db
-                    .prepare('SELECT COUNT(*) as c FROM embeddings WHERE node_id NOT IN (SELECT id FROM nodes)')
-                    .get().c;
-                if (orphaned > 0) {
-                    warn(`${orphaned} embeddings are orphaned (nodes changed). Run "codegraph embed" to refresh.`);
+    // Stale embeddings warning (built before current graph rebuild)
+    if (hasEmbeddings) {
+        try {
+            const embedBuiltAt = db.prepare("SELECT value FROM embedding_meta WHERE key = 'built_at'").get()?.value;
+            if (embedBuiltAt) {
+                const embedTime = new Date(embedBuiltAt).getTime();
+                if (!Number.isNaN(embedTime) && embedTime < buildNow.getTime()) {
+                    warn('Embeddings were built before the last graph rebuild. Run "codegraph embed" to update.');
                 }
             }
-            catch {
-                /* ignore - embeddings table may have been dropped */
-            }
         }
-        // Stale embeddings warning (built before current graph rebuild)
-        if (hasEmbeddings) {
-            try {
-                const embedBuiltAt = db.prepare("SELECT value FROM embedding_meta WHERE key = 'built_at'").get()?.value;
-                if (embedBuiltAt) {
-                    const embedTime = new Date(embedBuiltAt).getTime();
-                    if (!Number.isNaN(embedTime) && embedTime < buildNow.getTime()) {
-                        warn('Embeddings were built before the last graph rebuild. Run "codegraph embed" to update.');
-                    }
-                }
-            }
-            catch {
-                /* ignore - embedding_meta table may not exist */
-            }
+        catch {
+            /* ignore - embedding_meta table may not exist */
         }
-        // Unused exports warning
-        try {
-            const unusedCount = db
-                .prepare(`SELECT COUNT(*) as c FROM nodes
+    }
+    // Unused exports warning
+    try {
+        const unusedCount = db
+            .prepare(`SELECT COUNT(*) as c FROM nodes
          WHERE exported = 1 AND kind != 'file'
            AND id NOT IN (
              SELECT DISTINCT e.target_id FROM edges e
@@ -138,15 +135,37 @@ export async function finalize(ctx) {
              JOIN nodes target ON e.target_id = target.id
              WHERE e.kind = 'calls' AND caller.file != target.file
            )`)
-                .get().c;
-            if (unusedCount > 0) {
-                warn(`${unusedCount} exported symbol${unusedCount > 1 ? 's have' : ' has'} zero cross-file consumers. Run "codegraph exports <file> --unused" to inspect.`);
-            }
-        }
-        catch {
-            /* exported column may not exist on older DBs */
+            .get().c;
+        if (unusedCount > 0) {
+            warn(`${unusedCount} exported symbol${unusedCount > 1 ? 's have' : ' has'} zero cross-file consumers. Run "codegraph exports <file> --unused" to inspect.`);
         }
     }
+    catch {
+        /* exported column may not exist on older DBs */
+    }
+}
+export async function finalize(ctx) {
+    const { allSymbols, rootDir, isFullBuild, hasEmbeddings, opts } = ctx;
+    const t0 = performance.now();
+    releaseWasmTrees(allSymbols);
+    // Capture a single wall-clock timestamp for the current build — used for
+    // both the stale-embeddings comparison and the persisted built_at metadata.
+    const buildNow = new Date();
+    const nodeCount = ctx.db.prepare('SELECT COUNT(*) as c FROM nodes').get().c;
+    const actualEdgeCount = ctx.db.prepare('SELECT COUNT(*) as c FROM edges').get()
+        .c;
+    info(`Graph built: ${nodeCount} nodes, ${actualEdgeCount} edges`);
+    info(`Stored in ${ctx.dbPath}`);
+    detectIncrementalDrift(ctx, nodeCount, actualEdgeCount);
+    persistBuildMetadata(ctx, nodeCount, actualEdgeCount, buildNow);
+    // Skip expensive advisory queries for incremental builds — these are
+    // informational warnings that don't affect correctness and cost ~40-60ms.
+    if (!isFullBuild) {
+        debug('Finalize: skipping advisory queries (orphaned/stale embeddings, unused exports) for incremental build');
+    }
+    else {
+        runAdvisoryChecks(ctx.db, hasEmbeddings, buildNow);
+    }
     // Intentionally measured before closeDb / writeJournalHeader / auto-registration:
     // for the deferred-close path the close is async (setImmediate), and for full
     // builds the metric captures finalize logic only — DB close cost is tracked
@@ -156,7 +175,7 @@ export async function finalize(ctx) {
     // For small incremental builds, defer the expensive WAL checkpoint to the
     // next event loop tick. Skip for temp directories (tests) — they rmSync
     // immediately after build.
-    const pair = { db, nativeDb: ctx.nativeDb };
+    const pair = { db: ctx.db, nativeDb: ctx.nativeDb };
     const isTempDir = path.resolve(rootDir).startsWith(path.resolve(tmpdir()));
     if (!isFullBuild && allSymbols.size <= 5 && !isTempDir) {
         closeDbPairDeferred(pair);

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

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package/dist/domain/graph/builder/stages/insert-nodes.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"insert-nodes.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/insert-nodes.ts"],"names":[],"mappings":"AAmBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA8TrD,wBAAsB,WAAW,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAsDrE"}