@optave/codegraph 3.4.1 → 3.5.0

package/dist/db/repository/nodes.js.map

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

@@ -4,7 +4,7 @@
  * Each stage reads what it needs and writes what it produces.
  * This replaces the closure-captured locals in the old monolithic buildGraph().
  */
-import type { BetterSqlite3Database, BuildGraphOpts, CodegraphConfig, EngineOpts, ExtractorOutput, FileToParse, MetadataUpdate, NodeRow, ParseChange, PathAliases } from '../../../types.js';
+import type { BetterSqlite3Database, BuildGraphOpts, CodegraphConfig, EngineOpts, ExtractorOutput, FileToParse, MetadataUpdate, NativeDatabase, NodeRow, ParseChange, PathAliases } from '../../../types.js';
 export declare class PipelineContext {
     rootDir: string;
     db: BetterSqlite3Database;
@@ -18,6 +18,7 @@ export declare class PipelineContext {
     incremental: boolean;
     forceFullRebuild: boolean;
     schemaVersion: number;
+    nativeDb?: NativeDatabase;
     allFiles: string[];
     discoveredDirs: Set<string>;
     isFullBuild: boolean;

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

@@ -1 +1 @@
-{"version":3,"file":"context.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/context.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,KAAK,EACV,qBAAqB,EACrB,cAAc,EACd,eAAe,EACf,UAAU,EACV,eAAe,EACf,WAAW,EACX,cAAc,EACd,OAAO,EACP,WAAW,EACX,WAAW,EACZ,MAAM,mBAAmB,CAAC;AAE3B,qBAAa,eAAe;IAE1B,OAAO,EAAG,MAAM,CAAC;IACjB,EAAE,EAAG,qBAAqB,CAAC;IAC3B,MAAM,EAAG,MAAM,CAAC;IAChB,MAAM,EAAG,eAAe,CAAC;IACzB,IAAI,EAAG,cAAc,CAAC;IACtB,UAAU,EAAG,UAAU,CAAC;IACxB,UAAU,EAAG,QAAQ,GAAG,MAAM,CAAC;IAC/B,aAAa,EAAG,MAAM,GAAG,IAAI,CAAC;IAC9B,OAAO,EAAG,WAAW,CAAC;IACtB,WAAW,EAAG,OAAO,CAAC;IACtB,gBAAgB,EAAE,OAAO,CAAS;IAClC,aAAa,EAAG,MAAM,CAAC;IAGvB,QAAQ,EAAG,MAAM,EAAE,CAAC;IACpB,cAAc,EAAG,GAAG,CAAC,MAAM,CAAC,CAAC;IAG7B,WAAW,EAAG,OAAO,CAAC;IACtB,YAAY,EAAG,WAAW,EAAE,CAAC;IAC7B,eAAe,EAAG,cAAc,EAAE,CAAC;IACnC,OAAO,EAAG,MAAM,EAAE,CAAC;IACnB,SAAS,EAAE,OAAO,CAAS;IAG3B,UAAU,EAAG,GAAG,CAAC,MAAM,EAAE,eAAe,CAAC,CAAC;IAC1C,WAAW,EAAG,GAAG,CAAC,MAAM,EAAE,eAAe,CAAC,CAAC;IAC3C,YAAY,EAAG,WAAW,EAAE,CAAC;IAG7B,aAAa,EAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC;IAC3C,WAAW,EAAG,GAAG,CAAC,MAAM,EAAE,OAAO,EAAE,CAAC,CAAC;IACrC,eAAe,EAAG,GAAG,CAAC,MAAM,CAAC,CAAC;IAG9B,WAAW,EAAG,GAAG,CAAC,MAAM,EAAE,OAAO,EAAE,CAAC,CAAC;IACrC,kBAAkB,EAAG,GAAG,CAAC,MAAM,EAAE,OAAO,EAAE,CAAC,CAAC;IAG5C,aAAa,EAAE,OAAO,CAAS;IAC/B,YAAY,EAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAGnC,MAAM,EAAE;QACN,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;QAClB,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,WAAW,CAAC,EAAE,MAAM,CAAC;QACrB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,YAAY,CAAC,EAAE,MAAM,CAAC;QACtB,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAAC;KACnC,CAAM;IACP,UAAU,EAAG,MAAM,CAAC;CACrB"}
+{"version":3,"file":"context.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/context.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,KAAK,EACV,qBAAqB,EACrB,cAAc,EACd,eAAe,EACf,UAAU,EACV,eAAe,EACf,WAAW,EACX,cAAc,EACd,cAAc,EACd,OAAO,EACP,WAAW,EACX,WAAW,EACZ,MAAM,mBAAmB,CAAC;AAE3B,qBAAa,eAAe;IAE1B,OAAO,EAAG,MAAM,CAAC;IACjB,EAAE,EAAG,qBAAqB,CAAC;IAC3B,MAAM,EAAG,MAAM,CAAC;IAChB,MAAM,EAAG,eAAe,CAAC;IACzB,IAAI,EAAG,cAAc,CAAC;IACtB,UAAU,EAAG,UAAU,CAAC;IACxB,UAAU,EAAG,QAAQ,GAAG,MAAM,CAAC;IAC/B,aAAa,EAAG,MAAM,GAAG,IAAI,CAAC;IAC9B,OAAO,EAAG,WAAW,CAAC;IACtB,WAAW,EAAG,OAAO,CAAC;IACtB,gBAAgB,EAAE,OAAO,CAAS;IAClC,aAAa,EAAG,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,cAAc,CAAC;IAG1B,QAAQ,EAAG,MAAM,EAAE,CAAC;IACpB,cAAc,EAAG,GAAG,CAAC,MAAM,CAAC,CAAC;IAG7B,WAAW,EAAG,OAAO,CAAC;IACtB,YAAY,EAAG,WAAW,EAAE,CAAC;IAC7B,eAAe,EAAG,cAAc,EAAE,CAAC;IACnC,OAAO,EAAG,MAAM,EAAE,CAAC;IACnB,SAAS,EAAE,OAAO,CAAS;IAG3B,UAAU,EAAG,GAAG,CAAC,MAAM,EAAE,eAAe,CAAC,CAAC;IAC1C,WAAW,EAAG,GAAG,CAAC,MAAM,EAAE,eAAe,CAAC,CAAC;IAC3C,YAAY,EAAG,WAAW,EAAE,CAAC;IAG7B,aAAa,EAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC;IAC3C,WAAW,EAAG,GAAG,CAAC,MAAM,EAAE,OAAO,EAAE,CAAC,CAAC;IACrC,eAAe,EAAG,GAAG,CAAC,MAAM,CAAC,CAAC;IAG9B,WAAW,EAAG,GAAG,CAAC,MAAM,EAAE,OAAO,EAAE,CAAC,CAAC;IACrC,kBAAkB,EAAG,GAAG,CAAC,MAAM,EAAE,OAAO,EAAE,CAAC,CAAC;IAG5C,aAAa,EAAE,OAAO,CAAS;IAC/B,YAAY,EAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAGnC,MAAM,EAAE;QACN,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;QAClB,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,WAAW,CAAC,EAAE,MAAM,CAAC;QACrB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,YAAY,CAAC,EAAE,MAAM,CAAC;QACtB,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAAC;KACnC,CAAM;IACP,UAAU,EAAG,MAAM,CAAC;CACrB"}

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

@@ -12,6 +12,7 @@ export class PipelineContext {
     incremental;
     forceFullRebuild = false;
     schemaVersion;
+    nativeDb;
     // ── File collection (set by collectFiles stage) ────────────────────
     allFiles;
     discoveredDirs;

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

@@ -1 +1 @@
-{"version":3,"file":"context.js","sourceRoot":"","sources":["../../../../src/domain/graph/builder/context.ts"],"names":[],"mappings":"AAmBA,MAAM,OAAO,eAAe;IAC1B,sEAAsE;IACtE,OAAO,CAAU;IACjB,EAAE,CAAyB;IAC3B,MAAM,CAAU;IAChB,MAAM,CAAmB;IACzB,IAAI,CAAkB;IACtB,UAAU,CAAc;IACxB,UAAU,CAAqB;IAC/B,aAAa,CAAiB;IAC9B,OAAO,CAAe;IACtB,WAAW,CAAW;IACtB,gBAAgB,GAAY,KAAK,CAAC;IAClC,aAAa,CAAU;IAEvB,sEAAsE;IACtE,QAAQ,CAAY;IACpB,cAAc,CAAe;IAE7B,sEAAsE;IACtE,WAAW,CAAW;IACtB,YAAY,CAAiB;IAC7B,eAAe,CAAoB;IACnC,OAAO,CAAY;IACnB,SAAS,GAAY,KAAK,CAAC;IAE3B,sEAAsE;IACtE,UAAU,CAAgC;IAC1C,WAAW,CAAgC;IAC3C,YAAY,CAAiB;IAE7B,sEAAsE;IACtE,aAAa,CAA8B;IAC3C,WAAW,CAA0B;IACrC,eAAe,CAAe;IAE9B,sEAAsE;IACtE,WAAW,CAA0B;IACrC,kBAAkB,CAA0B;IAE5C,sEAAsE;IACtE,aAAa,GAAY,KAAK,CAAC;IAC/B,YAAY,CAAuB;IAEnC,sEAAsE;IACtE,MAAM,GAcF,EAAE,CAAC;IACP,UAAU,CAAU;CACrB"}
+{"version":3,"file":"context.js","sourceRoot":"","sources":["../../../../src/domain/graph/builder/context.ts"],"names":[],"mappings":"AAoBA,MAAM,OAAO,eAAe;IAC1B,sEAAsE;IACtE,OAAO,CAAU;IACjB,EAAE,CAAyB;IAC3B,MAAM,CAAU;IAChB,MAAM,CAAmB;IACzB,IAAI,CAAkB;IACtB,UAAU,CAAc;IACxB,UAAU,CAAqB;IAC/B,aAAa,CAAiB;IAC9B,OAAO,CAAe;IACtB,WAAW,CAAW;IACtB,gBAAgB,GAAY,KAAK,CAAC;IAClC,aAAa,CAAU;IACvB,QAAQ,CAAkB;IAE1B,sEAAsE;IACtE,QAAQ,CAAY;IACpB,cAAc,CAAe;IAE7B,sEAAsE;IACtE,WAAW,CAAW;IACtB,YAAY,CAAiB;IAC7B,eAAe,CAAoB;IACnC,OAAO,CAAY;IACnB,SAAS,GAAY,KAAK,CAAC;IAE3B,sEAAsE;IACtE,UAAU,CAAgC;IAC1C,WAAW,CAAgC;IAC3C,YAAY,CAAiB;IAE7B,sEAAsE;IACtE,aAAa,CAA8B;IAC3C,WAAW,CAA0B;IACrC,eAAe,CAAe;IAE9B,sEAAsE;IACtE,WAAW,CAA0B;IACrC,kBAAkB,CAA0B;IAE5C,sEAAsE;IACtE,aAAa,GAAY,KAAK,CAAC;IAC/B,YAAY,CAAuB;IAEnC,sEAAsE;IACtE,MAAM,GAcF,EAAE,CAAC;IACP,UAAU,CAAU;CACrB"}

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":"AAYA,OAAO,KAAK,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AA4IrE;;;;GAIG;AACH,wBAAsB,UAAU,CAC9B,OAAO,EAAE,MAAM,EACf,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,WAAW,GAAG,SAAS,CAAC,CAiBlC"}
+{"version":3,"file":"pipeline.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/pipeline.ts"],"names":[],"mappings":"AAaA,OAAO,KAAK,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAiKrE;;;;GAIG;AACH,wBAAsB,UAAU,CAC9B,OAAO,EAAE,MAAM,EACf,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,WAAW,GAAG,SAAS,CAAC,CAmBlC"}

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

@@ -6,9 +6,10 @@
  */
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { closeDb, getBuildMeta, initSchema, MIGRATIONS, openDb } from '../../../db/index.js';
+import { closeDbPair, getBuildMeta, initSchema, MIGRATIONS, openDb } from '../../../db/index.js';
 import { detectWorkspaces, loadConfig } from '../../../infrastructure/config.js';
 import { info, warn } from '../../../infrastructure/logger.js';
+import { loadNative } from '../../../infrastructure/native.js';
 import { CODEGRAPH_VERSION } from '../../../shared/version.js';
 import { getActiveEngine } from '../../parser.js';
 import { setWorkspaces } from '../resolve.js';
@@ -30,6 +31,7 @@ function initializeEngine(ctx) {
         engine: ctx.opts.engine || 'auto',
         dataflow: ctx.opts.dataflow !== false,
         ast: ctx.opts.ast !== false,
+        nativeDb: ctx.nativeDb,
     };
     const { name: engineName, version: engineVersion } = getActiveEngine(ctx.engineOpts);
     ctx.engineName = engineName;
@@ -42,17 +44,19 @@ function checkEngineSchemaMismatch(ctx) {
     ctx.forceFullRebuild = false;
     if (!ctx.incremental)
         return;
-    const prevEngine = getBuildMeta(ctx.db, 'engine');
+    // Route metadata reads through NativeDatabase when available (Phase 6.13)
+    const meta = (key) => ctx.nativeDb ? ctx.nativeDb.getBuildMeta(key) : getBuildMeta(ctx.db, key);
+    const prevEngine = meta('engine');
     if (prevEngine && prevEngine !== ctx.engineName) {
         info(`Engine changed (${prevEngine} → ${ctx.engineName}), promoting to full rebuild.`);
         ctx.forceFullRebuild = true;
     }
-    const prevSchema = getBuildMeta(ctx.db, 'schema_version');
+    const prevSchema = meta('schema_version');
     if (prevSchema && Number(prevSchema) !== ctx.schemaVersion) {
         info(`Schema version changed (${prevSchema} → ${ctx.schemaVersion}), promoting to full rebuild.`);
         ctx.forceFullRebuild = true;
     }
-    const prevVersion = getBuildMeta(ctx.db, 'codegraph_version');
+    const prevVersion = meta('codegraph_version');
     if (prevVersion && prevVersion !== CODEGRAPH_VERSION) {
         info(`Codegraph version changed (${prevVersion} → ${CODEGRAPH_VERSION}), promoting to full rebuild.`);
         ctx.forceFullRebuild = true;
@@ -79,7 +83,24 @@ function setupPipeline(ctx) {
     ctx.rootDir = path.resolve(ctx.rootDir);
     ctx.dbPath = path.join(ctx.rootDir, '.codegraph', 'graph.db');
     ctx.db = openDb(ctx.dbPath);
-    initSchema(ctx.db);
+    // Use NativeDatabase for schema init when native engine is available (Phase 6.13).
+    // better-sqlite3 (ctx.db) is still always opened — needed for queries and stages
+    // that haven't been migrated to rusqlite yet.
+    const native = loadNative();
+    if (native?.NativeDatabase) {
+        try {
+            ctx.nativeDb = native.NativeDatabase.openReadWrite(ctx.dbPath);
+            ctx.nativeDb.initSchema();
+        }
+        catch (err) {
+            warn(`NativeDatabase init failed, falling back to JS: ${err.message}`);
+            ctx.nativeDb = undefined;
+            initSchema(ctx.db);
+        }
+    }
+    else {
+        initSchema(ctx.db);
+    }
     ctx.config = loadConfig(ctx.rootDir);
     ctx.incremental =
         ctx.opts.incremental !== false && ctx.config.build && ctx.config.build.incremental !== false;
@@ -143,8 +164,9 @@ export async function buildGraph(rootDir, opts = {}) {
         await runPipelineStages(ctx);
     }
     catch (err) {
-        if (!ctx.earlyExit && ctx.db)
-            closeDb(ctx.db);
+        if (!ctx.earlyExit && ctx.db) {
+            closeDbPair({ db: ctx.db, nativeDb: ctx.nativeDb });
+        }
         throw err;
     }
     if (ctx.earlyExit)

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

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package/dist/domain/graph/builder/stages/build-edges.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"build-edges.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/build-edges.ts"],"names":[],"mappings":"AAqBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA8hBrD,wBAAsB,UAAU,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAwCpE"}
+{"version":3,"file":"build-edges.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/build-edges.ts"],"names":[],"mappings":"AAsBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAkmBrD,wBAAsB,UAAU,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAqEpE"}

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

@@ -6,8 +6,9 @@
  */
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { getNodeId } from '../../../../db/index.js';
-import { loadNative } from '../../../../infrastructure/native.js';
+import { getNodeId } from '#db/index.js';
+import { debug } from '#infrastructure/logger.js';
+import { loadNative } from '#infrastructure/native.js';
 import { computeConfidence } from '../../resolve.js';
 import { BUILTIN_RECEIVERS, batchInsertEdges } from '../helpers.js';
 import { getResolved, isBarrelFile, resolveBarrelExport } from './resolve-imports.js';
@@ -357,35 +358,122 @@ function buildClassHierarchyEdges(ctx, relPath, symbols, allEdgeRows) {
     }
 }
 // ── Main entry point ────────────────────────────────────────────────────
+/**
+ * For small incremental builds (≤5 changed files on a large codebase), scope
+ * the node loading query to only files that are relevant: changed files +
+ * their import targets. Falls back to loading ALL nodes for full builds or
+ * larger incremental changes.
+ */
+function loadNodes(ctx) {
+    const { db, fileSymbols, isFullBuild, batchResolved } = ctx;
+    const nodeKindFilter = `kind IN ('function','method','class','interface','struct','type','module','enum','trait','record','constant')`;
+    // Gate: only scope for small incremental on large codebases
+    if (!isFullBuild && fileSymbols.size <= 5) {
+        const existingFileCount = db.prepare("SELECT COUNT(*) as c FROM nodes WHERE kind = 'file'").get().c;
+        if (existingFileCount > 20) {
+            // Collect relevant files: changed files + their import targets
+            const relevantFiles = new Set(fileSymbols.keys());
+            if (batchResolved) {
+                for (const resolvedPath of batchResolved.values()) {
+                    relevantFiles.add(resolvedPath);
+                }
+            }
+            // Also add barrel-only files
+            for (const barrelPath of ctx.barrelOnlyFiles) {
+                relevantFiles.add(barrelPath);
+            }
+            const placeholders = [...relevantFiles].map(() => '?').join(',');
+            const rows = db
+                .prepare(`SELECT id, name, kind, file, line FROM nodes WHERE ${nodeKindFilter} AND file IN (${placeholders})`)
+                .all(...relevantFiles);
+            return { rows, scoped: true };
+        }
+    }
+    const rows = db
+        .prepare(`SELECT id, name, kind, file, line FROM nodes WHERE ${nodeKindFilter}`)
+        .all();
+    return { rows, scoped: false };
+}
+/**
+ * For scoped node loading, patch nodesByName.get with a lazy SQL fallback
+ * so global name-only lookups (resolveByMethodOrGlobal, supplementReceiverEdges)
+ * can still find nodes outside the scoped set.
+ */
+function addLazyFallback(ctx, scopedLoad) {
+    if (!scopedLoad)
+        return;
+    const { db } = ctx;
+    const fallbackStmt = db.prepare(`SELECT id, name, kind, file, line FROM nodes WHERE name = ? AND kind != 'file'`);
+    const originalGet = ctx.nodesByName.get.bind(ctx.nodesByName);
+    ctx.nodesByName.get = (name) => {
+        const result = originalGet(name);
+        if (result !== undefined)
+            return result;
+        const rows = fallbackStmt.all(name);
+        if (rows.length > 0) {
+            ctx.nodesByName.set(name, rows);
+            return rows;
+        }
+        return undefined;
+    };
+}
 export async function buildEdges(ctx) {
     const { db, engineName } = ctx;
     const getNodeIdStmt = makeGetNodeIdStmt(db);
-    const allNodes = db
-        .prepare(`SELECT id, name, kind, file, line FROM nodes WHERE kind IN ('function','method','class','interface','struct','type','module','enum','trait','record','constant')`)
-        .all();
-    setupNodeLookups(ctx, allNodes);
+    const { rows: allNodesBefore, scoped: scopedLoad } = loadNodes(ctx);
+    setupNodeLookups(ctx, allNodesBefore);
+    addLazyFallback(ctx, scopedLoad);
     const t0 = performance.now();
-    const buildEdgesTx = db.transaction(() => {
-        // Delete stale outgoing edges for barrel-only files inside the transaction
-        // so that deletion and re-creation are atomic (no edge loss on mid-build crash).
+    const native = engineName === 'native' ? loadNative() : null;
+    // Phase 1: Compute edges inside a better-sqlite3 transaction.
+    // Barrel-edge deletion lives here so that the JS path (which also inserts
+    // edges in this transaction) keeps deletion + insertion atomic.
+    // When using the native rusqlite path, insertion happens in Phase 2 on a
+    // separate connection — a crash between Phase 1 and Phase 2 would leave
+    // barrel edges missing until the next incremental rebuild re-creates them.
+    const allEdgeRows = [];
+    const computeEdgesTx = db.transaction(() => {
         if (ctx.barrelOnlyFiles.size > 0) {
             const deleteOutgoingEdges = db.prepare('DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE file = ?)');
             for (const relPath of ctx.barrelOnlyFiles) {
                 deleteOutgoingEdges.run(relPath);
             }
         }
-        const allEdgeRows = [];
         buildImportEdges(ctx, getNodeIdStmt, allEdgeRows);
-        const native = engineName === 'native' ? loadNative() : null;
-        if (native?.buildCallEdges) {
-            buildCallEdgesNative(ctx, getNodeIdStmt, allEdgeRows, allNodes, native);
+        // Skip native call-edge path for small incremental builds (≤3 files):
+        // napi-rs marshaling overhead for allNodes exceeds computation savings.
+        const useNativeCallEdges = native?.buildCallEdges && (ctx.isFullBuild || ctx.fileSymbols.size > 3);
+        if (useNativeCallEdges) {
+            buildCallEdgesNative(ctx, getNodeIdStmt, allEdgeRows, allNodesBefore, native);
         }
         else {
             buildCallEdgesJS(ctx, getNodeIdStmt, allEdgeRows);
         }
-        batchInsertEdges(db, allEdgeRows);
+        // When using native edge insert, skip JS insert here — do it after tx commits.
+        // Otherwise insert edges within this transaction for atomicity.
+        const useNativeEdgeInsert = !!ctx.nativeDb?.bulkInsertEdges;
+        if (!useNativeEdgeInsert) {
+            batchInsertEdges(db, allEdgeRows);
+        }
     });
-    buildEdgesTx();
+    computeEdgesTx();
+    // Phase 2: Native rusqlite bulk insert (outside better-sqlite3 transaction
+    // to avoid SQLITE_BUSY contention). Uses NativeDatabase persistent connection.
+    // Standalone napi functions were removed in 6.17.
+    if (ctx.nativeDb?.bulkInsertEdges && allEdgeRows.length > 0) {
+        const nativeEdges = allEdgeRows.map((r) => ({
+            sourceId: r[0],
+            targetId: r[1],
+            kind: r[2],
+            confidence: r[3],
+            dynamic: r[4],
+        }));
+        const ok = ctx.nativeDb.bulkInsertEdges(nativeEdges);
+        if (!ok) {
+            debug('Native bulkInsertEdges failed — falling back to JS batchInsertEdges');
+            batchInsertEdges(db, allEdgeRows);
+        }
+    }
     ctx.timing.edgesMs = performance.now() - t0;
 }
 //# sourceMappingURL=build-edges.js.map

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

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

@@ -1 +1 @@
-{"version":3,"file":"build-structure.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/build-structure.ts"],"names":[],"mappings":"AAUA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAGrD,wBAAsB,cAAc,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA6FxE"}
+{"version":3,"file":"build-structure.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/build-structure.ts"],"names":[],"mappings":"AAUA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAGrD,wBAAsB,cAAc,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAiIxE"}

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;
@@ -35,7 +35,9 @@ export async function buildStructure(ctx) {
     // Gate: ≤5 changed files AND significantly more existing files (>20) to
     // avoid triggering on small test fixtures where directory metrics matter.
     const existingFileCount = !isFullBuild
-        ? db.prepare("SELECT COUNT(*) as c FROM nodes WHERE kind = 'file'").get().c
+        ? (ctx.nativeDb
+            ? 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;
     const useSmallIncrementalFastPath = !isFullBuild &&
         changedFileList != null &&
@@ -68,8 +70,34 @@ export async function buildStructure(ctx) {
     // Classify node roles (incremental: only reclassify changed files' nodes)
     const t1 = performance.now();
     try {
-        const { classifyNodeRoles } = (await import('../../../../features/structure.js'));
-        const roleSummary = classifyNodeRoles(db, changedFileList);
+        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) {
+            const nativeResult = changedFileList && changedFileList.length > 0
+                ? ctx.nativeDb.classifyRolesIncremental(changedFileList)
+                : ctx.nativeDb.classifyRolesFull();
+            if (nativeResult) {
+                roleSummary = {
+                    entry: nativeResult.entry,
+                    core: nativeResult.core,
+                    utility: nativeResult.utility,
+                    adapter: nativeResult.adapter,
+                    dead: nativeResult.dead,
+                    'dead-leaf': nativeResult.deadLeaf,
+                    'dead-entry': nativeResult.deadEntry,
+                    'dead-ffi': nativeResult.deadFfi,
+                    'dead-unresolved': nativeResult.deadUnresolved,
+                    'test-only': nativeResult.testOnly,
+                    leaf: nativeResult.leaf,
+                };
+            }
+        }
+        // Fall back to JS path
+        if (!roleSummary) {
+            const { classifyNodeRoles } = (await import('../../../../features/structure.js'));
+            roleSummary = classifyNodeRoles(db, changedFileList);
+        }
         debug(`Roles${changedFileList ? ` (incremental, ${changedFileList.length} files)` : ''}: ${Object.entries(roleSummary)
             .map(([r, c]) => `${r}=${c}`)
             .join(', ')}`);

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

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

@@ -1 +1 @@
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