@optave/codegraph 3.4.0 → 3.5.0

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

@@ -14,10 +14,16 @@ import { parseFilesAuto } from '../../../parser.js';
 import { readJournal, writeJournalHeader } from '../../journal.js';
 import { fileHash, fileStat, purgeFilesFromGraph, readFileSafe } from '../helpers.js';
 // ── Helpers ────────────────────────────────────────────────────────────
-function getChangedFiles(db, allFiles, rootDir) {
+function getChangedFiles(db, allFiles, rootDir, nativeDb) {
     let hasTable = false;
     try {
-        db.prepare('SELECT 1 FROM file_hashes LIMIT 1').get();
+        if (nativeDb) {
+            nativeDb.queryGet('SELECT 1 FROM file_hashes LIMIT 1', []);
+        }
+        else {
+            db.prepare('SELECT 1 FROM file_hashes LIMIT 1').get();
+        }
+        // Query succeeded → table exists (result may be undefined if table is empty)
         hasTable = true;
     }
     catch {
@@ -30,7 +36,11 @@ function getChangedFiles(db, allFiles, rootDir) {
             isFullBuild: true,
         };
     }
-    const existing = new Map(db.prepare('SELECT file, hash, mtime, size FROM file_hashes').all().map((r) => [r.file, r]));
+    const sql = 'SELECT file, hash, mtime, size FROM file_hashes';
+    const rows = nativeDb
+        ? nativeDb.queryAll(sql, [])
+        : db.prepare(sql).all();
+    const existing = new Map(rows.map((r) => [r.file, r]));
     const removed = detectRemovedFiles(existing, allFiles, rootDir);
     const journalResult = tryJournalTier(db, existing, rootDir, removed);
     if (journalResult)
@@ -146,7 +156,7 @@ function mtimeAndHashTiers(existing, allFiles, rootDir, removed) {
 }
 async function runPendingAnalysis(ctx) {
     const { db, opts, engineOpts, allFiles, rootDir } = ctx;
-    const needsCfg = opts['cfg'] !== false &&
+    const needsCfg = opts.cfg !== false &&
         (() => {
             try {
                 return (db.prepare('SELECT COUNT(*) as c FROM cfg_blocks').get()
@@ -156,7 +166,7 @@ async function runPendingAnalysis(ctx) {
                 return true;
             }
         })();
-    const needsDataflow = opts['dataflow'] !== false &&
+    const needsDataflow = opts.dataflow !== false &&
         (() => {
             try {
                 return (db.prepare('SELECT COUNT(*) as c FROM dataflow').get()
@@ -171,7 +181,7 @@ async function runPendingAnalysis(ctx) {
     info('No file changes. Running pending analysis pass...');
     const analysisOpts = {
         ...engineOpts,
-        dataflow: needsDataflow && opts['dataflow'] !== false,
+        dataflow: needsDataflow && opts.dataflow !== false,
     };
     const analysisSymbols = await parseFilesAuto(allFiles, rootDir, analysisOpts);
     if (needsCfg) {
@@ -228,19 +238,31 @@ function findReverseDependencies(db, changedRelPaths, rootDir) {
 }
 function purgeAndAddReverseDeps(ctx, changePaths, reverseDeps) {
     const { db, rootDir } = ctx;
-    if (changePaths.length > 0 || ctx.removed.length > 0) {
-        purgeFilesFromGraph(db, [...ctx.removed, ...changePaths], { purgeHashes: false });
-    }
-    if (reverseDeps.size > 0) {
-        const deleteOutgoingEdgesForFile = db.prepare('DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE file = ?)');
-        for (const relPath of reverseDeps) {
-            deleteOutgoingEdgesForFile.run(relPath);
+    const hasPurge = changePaths.length > 0 || ctx.removed.length > 0;
+    const hasReverseDeps = reverseDeps.size > 0;
+    const reverseDepList = hasReverseDeps ? [...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) {
+            ctx.nativeDb.purgeFilesData(filesToPurge, false, hasReverseDeps ? reverseDepList : undefined);
         }
-        for (const relPath of reverseDeps) {
-            const absPath = path.join(rootDir, relPath);
-            ctx.parseChanges.push({ file: absPath, relPath, _reverseDepOnly: true });
+        else {
+            if (hasPurge) {
+                purgeFilesFromGraph(db, filesToPurge, { purgeHashes: false });
+            }
+            if (hasReverseDeps) {
+                const deleteOutgoingEdgesForFile = db.prepare('DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE file = ?)');
+                for (const relPath of reverseDepList) {
+                    deleteOutgoingEdgesForFile.run(relPath);
+                }
+            }
         }
     }
+    for (const relPath of reverseDeps) {
+        const absPath = path.join(rootDir, relPath);
+        ctx.parseChanges.push({ file: absPath, relPath, _reverseDepOnly: true });
+    }
 }
 function detectHasEmbeddings(db) {
     try {
@@ -256,7 +278,7 @@ function handleScopedBuild(ctx) {
     ctx.hasEmbeddings = detectHasEmbeddings(db);
     const changePaths = ctx.parseChanges.map((item) => item.relPath || normalizePath(path.relative(rootDir, item.file)));
     let reverseDeps = new Set();
-    if (!opts['noReverseDeps']) {
+    if (!opts.noReverseDeps) {
         const changedRelPaths = new Set([...changePaths, ...ctx.removed]);
         reverseDeps = findReverseDependencies(db, changedRelPaths, rootDir);
     }
@@ -276,7 +298,7 @@ function handleIncrementalBuild(ctx) {
     const { db, rootDir, opts } = ctx;
     ctx.hasEmbeddings = detectHasEmbeddings(db);
     let reverseDeps = new Set();
-    if (!opts['noReverseDeps']) {
+    if (!opts.noReverseDeps) {
         const changedRelPaths = new Set();
         for (const item of ctx.parseChanges) {
             changedRelPaths.add(item.relPath || normalizePath(path.relative(rootDir, item.file)));
@@ -296,12 +318,12 @@ function handleIncrementalBuild(ctx) {
 }
 export async function detectChanges(ctx) {
     const { db, allFiles, rootDir, incremental, forceFullRebuild, opts } = ctx;
-    if (opts['scope']) {
+    if (opts.scope) {
         handleScopedBuild(ctx);
         return;
     }
     const increResult = incremental && !forceFullRebuild
-        ? getChangedFiles(db, allFiles, rootDir)
+        ? getChangedFiles(db, allFiles, rootDir, ctx.nativeDb)
         : {
             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":"AAWA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AASrD,wBAAsB,QAAQ,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA4JlE"}
+{"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"}

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

@@ -3,14 +3,13 @@
  *
  * 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';
-import { closeDb, getBuildMeta, setBuildMeta } from '../../../../db/index.js';
+import { closeDbPair, closeDbPairDeferred, getBuildMeta, setBuildMeta, } from '../../../../db/index.js';
 import { debug, info, warn } from '../../../../infrastructure/logger.js';
+import { CODEGRAPH_VERSION } from '../../../../shared/version.js';
 import { writeJournalHeader } from '../../journal.js';
-const __builderDir = path.dirname(new URL(import.meta.url).pathname.replace(/^\/([A-Z]:)/i, '$1'));
-const CODEGRAPH_VERSION = JSON.parse(fs.readFileSync(path.join(__builderDir, '..', '..', '..', '..', '..', 'package.json'), 'utf-8')).version;
 export async function finalize(ctx) {
     const { db, allSymbols, rootDir, isFullBuild, hasEmbeddings, config, opts, schemaVersion } = ctx;
     const t0 = performance.now();
@@ -35,10 +34,15 @@ export async function finalize(ctx) {
     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
-    if (!isFullBuild) {
-        const prevNodes = getBuildMeta(db, 'node_count');
-        const prevEdges = getBuildMeta(db, 'edge_count');
+    // 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);
@@ -52,76 +56,120 @@ export async function finalize(ctx) {
             }
         }
     }
-    // Persist build metadata early so downstream checks (e.g. stale-embeddings)
-    // can read the *current* build's built_at rather than the previous one.
-    try {
-        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,
-        });
-    }
-    catch (err) {
-        warn(`Failed to write build metadata: ${err.message}`);
-    }
-    // Orphaned embeddings warning
-    if (hasEmbeddings) {
+    // For small incremental builds, skip persisting build metadata — the
+    // engine/version/schema haven't changed (would have triggered a full rebuild),
+    // built_at is only used by stale-embeddings check (skipped for incremental),
+    // and counts are only used by drift detection (skipped for ≤3 files).
+    // This avoids a transaction commit + WAL fsync (~15-30ms).
+    // Threshold aligned with drift detection gate (allSymbols.size > 3) so stored
+    // counts stay fresh whenever drift detection reads them.
+    if (isFullBuild || allSymbols.size > 3) {
         try {
-            const orphaned = db
-                .prepare('SELECT COUNT(*) as c FROM embeddings WHERE node_id NOT IN (SELECT id FROM nodes)')
-                .get().c;
-            if (orphaned > 0) {
-                warn(`${orphaned} embeddings are orphaned (nodes changed). Run "codegraph embed" to refresh.`);
+            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,
+                });
             }
         }
-        catch {
-            /* ignore - embeddings table may have been dropped */
+        catch (err) {
+            warn(`Failed to write build metadata: ${err.message}`);
         }
     }
-    // Stale embeddings warning (built before current graph rebuild)
-    if (hasEmbeddings) {
-        try {
-            const embedBuiltAt = db.prepare("SELECT value FROM embedding_meta WHERE key = 'built_at'").get()?.value;
-            if (embedBuiltAt) {
-                const embedTime = new Date(embedBuiltAt).getTime();
-                if (!Number.isNaN(embedTime) && embedTime < buildNow.getTime()) {
-                    warn('Embeddings were built before the last graph rebuild. Run "codegraph embed" to update.');
+    // Skip expensive advisory queries for incremental builds — these are
+    // informational warnings that don't affect correctness and cost ~40-60ms.
+    if (!isFullBuild) {
+        debug('Finalize: skipping advisory queries (orphaned/stale embeddings, unused exports) for incremental build');
+    }
+    else {
+        // Orphaned embeddings warning
+        if (hasEmbeddings) {
+            try {
+                const orphaned = db
+                    .prepare('SELECT COUNT(*) as c FROM embeddings WHERE node_id NOT IN (SELECT id FROM nodes)')
+                    .get().c;
+                if (orphaned > 0) {
+                    warn(`${orphaned} embeddings are orphaned (nodes changed). Run "codegraph embed" to refresh.`);
                 }
             }
+            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 */
+            }
+        }
+        // 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
+             JOIN nodes caller ON e.source_id = caller.id
+             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 {
-            /* ignore - embedding_meta table may not exist */
+            /* exported column may not exist on older DBs */
         }
     }
-    // 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
-           JOIN nodes caller ON e.source_id = caller.id
-           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.`);
-        }
+    // 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
+    // separately via timing.closeDbMs when available.
+    ctx.timing.finalizeMs = performance.now() - t0;
+    // Close NativeDatabase (fast, ~1ms) then better-sqlite3 (WAL checkpoint).
+    // 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 isTempDir = path.resolve(rootDir).startsWith(path.resolve(tmpdir()));
+    if (!isFullBuild && allSymbols.size <= 5 && !isTempDir) {
+        closeDbPairDeferred(pair);
     }
-    catch {
-        /* exported column may not exist on older DBs */
+    else {
+        closeDbPair(pair);
     }
-    closeDb(db);
     // Write journal header after successful build
     writeJournalHeader(rootDir, Date.now());
-    // Auto-registration
-    if (!opts.skipRegistry) {
-        const { tmpdir } = await import('node:os');
+    // Skip auto-registration for incremental builds — the repo was already
+    // registered during the initial full build. The dynamic import + file I/O
+    // costs ~100ms which dominates incremental finalize time.
+    if (!opts.skipRegistry && isFullBuild) {
         const tmpDir = path.resolve(tmpdir());
         const resolvedRoot = path.resolve(rootDir);
         if (resolvedRoot.startsWith(tmpDir)) {
@@ -137,6 +185,5 @@ export async function finalize(ctx) {
             }
         }
     }
-    ctx.timing.finalizeMs = performance.now() - t0;
 }
 //# sourceMappingURL=finalize.js.map

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 @@
-{"version":3,"file":"insert-nodes.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/insert-nodes.ts"],"names":[],"mappings":"AAWA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA+MrD,wBAAsB,WAAW,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAuCrE"}
+{"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;AAwTrD,wBAAsB,WAAW,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAiDrE"}

package/dist/domain/graph/builder/stages/insert-nodes.js

@@ -3,12 +3,100 @@
  *
  * Batch-inserts file nodes, definitions, exports, children, and contains/parameter_of edges.
  * Updates file hashes for incremental builds.
+ *
+ * When the native engine is available, delegates all SQLite writes to Rust via
+ * `bulkInsertNodes` — eliminating JS↔C boundary overhead. Falls back to the
+ * JS implementation on failure or when native is unavailable.
  */
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
 import { bulkNodeIdsByFile } from '../../../../db/index.js';
 import { batchInsertEdges, batchInsertNodes, fileHash, fileStat, readFileSafe, } from '../helpers.js';
-// ── Phase 1: Insert file nodes, definitions, exports ────────────────────
+// ── Native fast-path ─────────────────────────────────────────────────
+function tryNativeInsert(ctx) {
+    // 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?.bulkInsertNodes)
+        return false;
+    const { allSymbols, filesToParse, metadataUpdates, rootDir, removed } = ctx;
+    // Marshal allSymbols → InsertNodesBatch[]
+    const batches = [];
+    for (const [relPath, symbols] of allSymbols) {
+        batches.push({
+            file: relPath,
+            definitions: symbols.definitions.map((def) => ({
+                name: def.name,
+                kind: def.kind,
+                line: def.line,
+                endLine: def.endLine ?? null,
+                visibility: def.visibility ?? null,
+                children: (def.children ?? []).map((c) => ({
+                    name: c.name,
+                    kind: c.kind,
+                    line: c.line,
+                    endLine: c.endLine ?? null,
+                    visibility: c.visibility ?? null,
+                })),
+            })),
+            exports: symbols.exports.map((exp) => ({
+                name: exp.name,
+                kind: exp.kind,
+                line: exp.line,
+            })),
+        });
+    }
+    // Build file hash entries
+    const precomputedData = new Map();
+    for (const item of filesToParse) {
+        if (item.relPath)
+            precomputedData.set(item.relPath, item);
+    }
+    const fileHashes = [];
+    for (const [relPath] of allSymbols) {
+        const precomputed = precomputedData.get(relPath);
+        if (precomputed?._reverseDepOnly) {
+            continue; // file unchanged, hash already correct
+        }
+        if (precomputed?.hash) {
+            let mtime;
+            let size;
+            if (precomputed.stat) {
+                mtime = precomputed.stat.mtime;
+                size = precomputed.stat.size;
+            }
+            else {
+                const rawStat = fileStat(path.join(rootDir, relPath));
+                mtime = rawStat ? Math.floor(rawStat.mtimeMs) : 0;
+                size = rawStat ? rawStat.size : 0;
+            }
+            fileHashes.push({ file: relPath, hash: precomputed.hash, mtime, size });
+        }
+        else {
+            const absPath = path.join(rootDir, relPath);
+            let code;
+            try {
+                code = readFileSafe(absPath);
+            }
+            catch {
+                code = null;
+            }
+            if (code !== null) {
+                const stat = fileStat(absPath);
+                const mtime = stat ? Math.floor(stat.mtimeMs) : 0;
+                const size = stat ? stat.size : 0;
+                fileHashes.push({ file: relPath, hash: fileHash(code), mtime, size });
+            }
+        }
+    }
+    // Also include metadata-only updates (self-heal mtime/size without re-parse)
+    for (const item of metadataUpdates) {
+        const mtime = item.stat ? Math.floor(item.stat.mtime) : 0;
+        const size = item.stat ? item.stat.size : 0;
+        fileHashes.push({ file: item.relPath, hash: item.hash, mtime, size });
+    }
+    return ctx.nativeDb.bulkInsertNodes(batches, fileHashes, removed);
+}
+// ── JS fallback: Phase 1 ────────────────────────────────────────────
 function insertDefinitionsAndExports(db, allSymbols) {
     const phase1Rows = [];
     const exportKeys = [];
@@ -57,7 +145,7 @@ function insertDefinitionsAndExports(db, allSymbols) {
         }
     }
 }
-// ── Phase 2+3: Insert children and containment edges (two nodeIdMap passes) ──
+// ── JS fallback: Phase 2+3 ──────────────────────────────────────────
 function insertChildrenAndEdges(db, allSymbols) {
     const childRows = [];
     const edgeRows = [];
@@ -122,7 +210,7 @@ function insertChildrenAndEdges(db, allSymbols) {
     }
     batchInsertEdges(db, edgeRows);
 }
-// ── Phase 4: Update file hashes ─────────────────────────────────────────
+// ── JS fallback: Phase 4 ────────────────────────────────────────────
 function updateFileHashes(_db, allSymbols, precomputedData, metadataUpdates, rootDir, upsertHash) {
     if (!upsertHash)
         return;
@@ -169,9 +257,21 @@ function updateFileHashes(_db, allSymbols, precomputedData, metadataUpdates, roo
         upsertHash.run(item.relPath, item.hash, mtime, size);
     }
 }
-// ── Main entry point ────────────────────────────────────────────────────
+// ── Main entry point ────────────────────────────────────────────────
 export async function insertNodes(ctx) {
     const { db, allSymbols, filesToParse, metadataUpdates, rootDir, removed } = ctx;
+    // Populate fileSymbols before any DB writes (used by later stages)
+    for (const [relPath, symbols] of allSymbols) {
+        ctx.fileSymbols.set(relPath, symbols);
+    }
+    const t0 = performance.now();
+    // Try native Rust path first — single transaction, no JS↔C overhead
+    if (ctx.engineName === 'native' && tryNativeInsert(ctx)) {
+        ctx.timing.insertMs = performance.now() - t0;
+        // Removed-file hash cleanup is handled inside the native call
+        return;
+    }
+    // JS fallback
     const precomputedData = new Map();
     for (const item of filesToParse) {
         if (item.relPath)
@@ -184,16 +284,11 @@ export async function insertNodes(ctx) {
     catch {
         upsertHash = null;
     }
-    // Populate fileSymbols before the transaction so it is a pure input
-    for (const [relPath, symbols] of allSymbols) {
-        ctx.fileSymbols.set(relPath, symbols);
-    }
     const insertAll = db.transaction(() => {
         insertDefinitionsAndExports(db, allSymbols);
         insertChildrenAndEdges(db, allSymbols);
         updateFileHashes(db, allSymbols, precomputedData, metadataUpdates, rootDir, upsertHash);
     });
-    const t0 = performance.now();
     insertAll();
     ctx.timing.insertMs = performance.now() - t0;
     // Clean up removed file hashes