@optave/codegraph 3.5.0 → 3.6.0

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 @@
-{"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"}
+{"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"}

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

@@ -14,6 +14,12 @@ import { bulkNodeIdsByFile } from '../../../../db/index.js';
 import { batchInsertEdges, batchInsertNodes, fileHash, fileStat, readFileSafe, } from '../helpers.js';
 // ── Native fast-path ─────────────────────────────────────────────────
 function tryNativeInsert(ctx) {
+    // Disabled: bulkInsertNodes corrupts the DB when both the JS (better-sqlite3)
+    // and Rust (rusqlite) connections are open to the same WAL-mode file.
+    // The native path was never operational before — it always crashed on null
+    // visibility serialisation. See #696 for the dual-connection fix.
+    if (ctx.db)
+        return false;
     // 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)
@@ -28,14 +34,14 @@ function tryNativeInsert(ctx) {
                 name: def.name,
                 kind: def.kind,
                 line: def.line,
-                endLine: def.endLine ?? null,
-                visibility: def.visibility ?? null,
+                endLine: def.endLine ?? undefined,
+                visibility: def.visibility ?? undefined,
                 children: (def.children ?? []).map((c) => ({
                     name: c.name,
                     kind: c.kind,
                     line: c.line,
-                    endLine: c.endLine ?? null,
-                    visibility: c.visibility ?? null,
+                    endLine: c.endLine ?? undefined,
+                    visibility: c.visibility ?? undefined,
                 })),
             })),
             exports: symbols.exports.map((exp) => ({
@@ -259,17 +265,24 @@ function updateFileHashes(_db, allSymbols, precomputedData, metadataUpdates, roo
 }
 // ── Main entry point ────────────────────────────────────────────────
 export async function insertNodes(ctx) {
-    const { db, allSymbols, filesToParse, metadataUpdates, rootDir, removed } = ctx;
+    const { 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;
+    if (ctx.engineName === 'native') {
+        try {
+            if (tryNativeInsert(ctx)) {
+                ctx.timing.insertMs = performance.now() - t0;
+                // Removed-file hash cleanup is handled inside the native call
+                return;
+            }
+        }
+        catch {
+            // Native insert failed — fall through to JS implementation
+        }
     }
     // JS fallback
     const precomputedData = new Map();
@@ -279,21 +292,21 @@ export async function insertNodes(ctx) {
     }
     let upsertHash;
     try {
-        upsertHash = db.prepare('INSERT OR REPLACE INTO file_hashes (file, hash, mtime, size) VALUES (?, ?, ?, ?)');
+        upsertHash = ctx.db.prepare('INSERT OR REPLACE INTO file_hashes (file, hash, mtime, size) VALUES (?, ?, ?, ?)');
     }
     catch {
         upsertHash = null;
     }
-    const insertAll = db.transaction(() => {
-        insertDefinitionsAndExports(db, allSymbols);
-        insertChildrenAndEdges(db, allSymbols);
-        updateFileHashes(db, allSymbols, precomputedData, metadataUpdates, rootDir, upsertHash);
+    const insertAll = ctx.db.transaction(() => {
+        insertDefinitionsAndExports(ctx.db, allSymbols);
+        insertChildrenAndEdges(ctx.db, allSymbols);
+        updateFileHashes(ctx.db, allSymbols, precomputedData, metadataUpdates, rootDir, upsertHash);
     });
     insertAll();
     ctx.timing.insertMs = performance.now() - t0;
     // Clean up removed file hashes
     if (upsertHash && removed.length > 0) {
-        const deleteHash = db.prepare('DELETE FROM file_hashes WHERE file = ?');
+        const deleteHash = ctx.db.prepare('DELETE FROM file_hashes WHERE file = ?');
         for (const relPath of removed) {
             deleteHash.run(relPath);
         }

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

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

@@ -1 +1 @@
-{"version":3,"file":"resolve-imports.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/resolve-imports.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAQrD,wBAAsB,cAAc,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA8HxE;AAED,wBAAgB,WAAW,CAAC,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,MAAM,CAO/F;AAED,wBAAgB,YAAY,CAAC,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,MAAM,GAAG,OAAO,CAO3E;AAED,wBAAgB,mBAAmB,CACjC,GAAG,EAAE,eAAe,EACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,EAClB,OAAO,GAAE,GAAG,CAAC,MAAM,CAAqB,GACvC,MAAM,GAAG,IAAI,CA8Bf"}
+{"version":3,"file":"resolve-imports.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/resolve-imports.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAQrD,wBAAsB,cAAc,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA8HxE;AAED,wBAAgB,WAAW,CAAC,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,MAAM,CAO/F;AAED,wBAAgB,YAAY,CAAC,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,MAAM,GAAG,OAAO,CAO3E;AAED,wBAAgB,mBAAmB,CACjC,GAAG,EAAE,eAAe,EACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,EAClB,OAAO,GAAE,GAAG,CAAC,MAAM,CAAqB,GACvC,MAAM,GAAG,IAAI,CA8Bf"}

package/dist/domain/graph/builder/stages/resolve-imports.js

@@ -1,5 +1,6 @@
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
+import { debug } from '../../../../infrastructure/logger.js';
 import { parseFilesAuto } from '../../../parser.js';
 import { resolveImportPath, resolveImportsBatch } from '../../resolve.js';
 export async function resolveImports(ctx) {
@@ -99,8 +100,8 @@ export async function resolveImports(ctx) {
                     }
                 }
             }
-            catch {
-                /* skip if unreadable */
+            catch (e) {
+                debug(`Barrel re-parse failed (non-fatal): ${e.message}`);
             }
         }
     }

package/dist/domain/graph/builder/stages/resolve-imports.js.map

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

@@ -6,10 +6,6 @@ import type { BareSpecifier, BatchResolvedMap, ImportBatchItem, PathAliases } fr
  * No sub: "pkg"            → { packageName: "pkg", subpath: "." }
  */
 export declare function parseBareSpecifier(specifier: string): BareSpecifier | null;
-/**
- * Resolve a bare specifier through the package.json exports field.
- * Returns an absolute path or null.
- */
 export declare function resolveViaExports(specifier: string, rootDir: string): string | null;
 /** Clear the exports cache (for testing). */
 export declare function clearExportsCache(): void;