@optave/codegraph 3.4.1 → 3.6.0

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 +31,19 @@ function initializeEngine(ctx) {
         engine: ctx.opts.engine || 'auto',
         dataflow: ctx.opts.dataflow !== false,
         ast: ctx.opts.ast !== false,
+        nativeDb: ctx.nativeDb,
+        // WAL checkpoint callbacks for dual-connection WAL guard (#696).
+        // Feature modules (ast, cfg, complexity, dataflow) receive `db` as a
+        // parameter and cannot tolerate close/reopen (stale reference). Instead,
+        // checkpoint the WAL so native writes start with a clean slate. Features
+        // return early on native success and never read native-written WAL data
+        // through the JS connection, so a post-write checkpoint is unnecessary.
+        suspendJsDb: ctx.nativeDb
+            ? () => {
+                ctx.db.pragma('wal_checkpoint(TRUNCATE)');
+            }
+            : undefined,
+        resumeJsDb: ctx.nativeDb ? () => { } : undefined,
     };
     const { name: engineName, version: engineVersion } = getActiveEngine(ctx.engineOpts);
     ctx.engineName = engineName;
@@ -42,17 +56,21 @@ function checkEngineSchemaMismatch(ctx) {
     ctx.forceFullRebuild = false;
     if (!ctx.incremental)
         return;
-    const prevEngine = getBuildMeta(ctx.db, 'engine');
+    // Route metadata reads through NativeDatabase only when using the native engine,
+    // to avoid dual-SQLite WAL conflicts (rusqlite + better-sqlite3 on same file).
+    const useNativeDb = ctx.engineName === 'native' && !!ctx.nativeDb;
+    const meta = (key) => useNativeDb ? 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 +97,26 @@ 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;
+        }
+        // Always run JS initSchema so better-sqlite3 sees the schema —
+        // nativeDb is closed during pipeline stages and reopened for analyses.
+        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;
@@ -115,6 +152,26 @@ function formatTimingResult(ctx) {
 }
 // ── Pipeline stages execution ───────────────────────────────────────────
 async function runPipelineStages(ctx) {
+    // Prevent dual-connection WAL corruption during pipeline stages: when both
+    // better-sqlite3 (ctx.db) and rusqlite (ctx.nativeDb) are open to the same
+    // WAL-mode file, native writes corrupt the DB. Close nativeDb so stages
+    // use JS fallback paths. Reopened before runAnalyses for feature modules
+    // that use suspendJsDb/resumeJsDb WAL checkpoint pattern (#696).
+    const hadNativeDb = !!ctx.nativeDb;
+    if (ctx.db && ctx.nativeDb) {
+        try {
+            ctx.nativeDb.close();
+        }
+        catch {
+            /* ignore close errors */
+        }
+        ctx.nativeDb = undefined;
+        // Also clear stale reference in engineOpts to prevent stages from
+        // calling methods on the closed NativeDatabase.
+        if (ctx.engineOpts?.nativeDb) {
+            ctx.engineOpts.nativeDb = undefined;
+        }
+    }
     await collectFiles(ctx);
     await detectChanges(ctx);
     if (ctx.earlyExit)
@@ -124,7 +181,37 @@ async function runPipelineStages(ctx) {
     await resolveImports(ctx);
     await buildEdges(ctx);
     await buildStructure(ctx);
+    // Reopen nativeDb for feature modules (ast, cfg, complexity, dataflow)
+    // which use suspendJsDb/resumeJsDb WAL checkpoint before native writes.
+    if (hadNativeDb) {
+        const native = loadNative();
+        if (native?.NativeDatabase) {
+            try {
+                ctx.nativeDb = native.NativeDatabase.openReadWrite(ctx.dbPath);
+                if (ctx.engineOpts) {
+                    ctx.engineOpts.nativeDb = ctx.nativeDb;
+                }
+            }
+            catch {
+                ctx.nativeDb = undefined;
+                if (ctx.engineOpts) {
+                    ctx.engineOpts.nativeDb = undefined;
+                }
+            }
+        }
+    }
     await runAnalyses(ctx);
+    // Close nativeDb after analyses — finalize uses JS paths for setBuildMeta
+    // and closeDbPair handles cleanup. Avoids dual-connection during finalize.
+    if (ctx.nativeDb) {
+        try {
+            ctx.nativeDb.close();
+        }
+        catch {
+            /* ignore close errors */
+        }
+        ctx.nativeDb = undefined;
+    }
     await finalize(ctx);
 }
 // ── Main entry point ────────────────────────────────────────────────────
@@ -143,8 +230,9 @@ 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

@@ -1 +1 @@
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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;AAiiBrD,wBAAsB,UAAU,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAqEpE"}

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

@@ -7,6 +7,7 @@
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
 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';
@@ -126,13 +127,6 @@ function buildCallEdgesNative(ctx, getNodeIdStmt, allEdgeRows, allNodes, native)
     for (const e of nativeEdges) {
         allEdgeRows.push([e.sourceId, e.targetId, e.kind, e.confidence, e.dynamic]);
     }
-    // Older native binaries (< 3.2.0) don't emit receiver or type-resolved method-call
-    // edges. Supplement them on the JS side if the native binary missed them.
-    // TODO: Remove once all published native binaries handle receivers (>= 3.2.0)
-    const hasReceiver = nativeEdges.some((e) => e.kind === 'receiver');
-    if (!hasReceiver) {
-        supplementReceiverEdges(ctx, nativeFiles, getNodeIdStmt, allEdgeRows);
-    }
 }
 function buildImportedNamesForNative(ctx, relPath, symbols, rootDir) {
     const importedNames = [];
@@ -151,43 +145,6 @@ function buildImportedNamesForNative(ctx, relPath, symbols, rootDir) {
     }
     return importedNames;
 }
-// ── Receiver edge supplement for older native binaries ──────────────────
-function supplementReceiverEdges(ctx, nativeFiles, getNodeIdStmt, allEdgeRows) {
-    const seenCallEdges = new Set();
-    // Collect existing edges to avoid duplicates
-    for (const row of allEdgeRows) {
-        seenCallEdges.add(`${row[0]}|${row[1]}|${row[2]}`);
-    }
-    for (const nf of nativeFiles) {
-        const relPath = nf.file;
-        const typeMap = new Map(nf.typeMap.map((t) => [t.name, { type: t.typeName, confidence: t.confidence ?? 0.9 }]));
-        const fileNodeRow = { id: nf.fileNodeId };
-        for (const call of nf.calls) {
-            if (!call.receiver || BUILTIN_RECEIVERS.has(call.receiver))
-                continue;
-            if (call.receiver === 'this' || call.receiver === 'self' || call.receiver === 'super')
-                continue;
-            const caller = findCaller(call, nf.definitions, relPath, getNodeIdStmt, fileNodeRow);
-            // Receiver edge: caller → receiver type node
-            buildReceiverEdge(ctx, call, caller, relPath, seenCallEdges, allEdgeRows, typeMap);
-            // Type-resolved method call: caller → Type.method
-            const typeEntry = typeMap.get(call.receiver);
-            const typeName = typeEntry ? typeEntry.type : null;
-            if (typeName) {
-                const qualifiedName = `${typeName}.${call.name}`;
-                const targets = (ctx.nodesByName.get(qualifiedName) || []).filter((n) => n.kind === 'method');
-                for (const t of targets) {
-                    const key = `${caller.id}|${t.id}|calls`;
-                    if (t.id !== caller.id && !seenCallEdges.has(key)) {
-                        seenCallEdges.add(key);
-                        const confidence = computeConfidence(relPath, t.file, null);
-                        allEdgeRows.push([caller.id, t.id, 'calls', confidence, call.dynamic ? 1 : 0]);
-                    }
-                }
-            }
-        }
-    }
-}
 // ── Call edges (JS fallback) ────────────────────────────────────────────
 function buildCallEdgesJS(ctx, getNodeIdStmt, allEdgeRows) {
     const { fileSymbols, barrelOnlyFiles, rootDir } = ctx;
@@ -357,35 +314,122 @@ 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)
+ * 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.engineName === 'native' && !!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.engineName === 'native' && 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(ctx.db, allEdgeRows);
+        }
+    }
     ctx.timing.edgesMs = performance.now() - t0;
 }
 //# sourceMappingURL=build-edges.js.map

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

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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,CAmIxE"}

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

@@ -34,8 +34,11 @@ 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
-        ? db.prepare("SELECT COUNT(*) as c FROM nodes WHERE kind = 'file'").get().c
+        ? (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;
     const useSmallIncrementalFastPath = !isFullBuild &&
         changedFileList != null &&
@@ -68,8 +71,35 @@ 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.
+        // 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();
+            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(ctx.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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