@optave/codegraph 3.3.1 → 3.4.1

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

@@ -3,37 +3,40 @@
  *
  * 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 { closeDb, closeDbDeferred, 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;
-/**
- * @param {import('../context.js').PipelineContext} ctx
- */
 export async function finalize(ctx) {
     const { db, allSymbols, rootDir, isFullBuild, hasEmbeddings, config, opts, schemaVersion } = ctx;
     const t0 = performance.now();
     // Release cached WASM trees
     for (const [, symbols] of allSymbols) {
-        if (symbols._tree && typeof symbols._tree.delete === 'function') {
+        const tree = symbols._tree;
+        if (tree && typeof tree.delete === 'function') {
             try {
-                symbols._tree.delete();
+                tree.delete();
+            }
+            catch {
+                /* ignore cleanup errors */
             }
-            catch { }
         }
-        symbols._tree = null;
-        symbols._langId = null;
+        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
-    if (!isFullBuild) {
+    // Incremental drift detection — skip for small incremental changes where
+    // count fluctuation is expected (reverse-dep edge churn).
+    if (!isFullBuild && allSymbols.size > 3) {
         const prevNodes = getBuildMeta(db, 'node_count');
         const prevEdges = getBuildMeta(db, 'edge_count');
         if (prevNodes && prevEdges) {
@@ -44,64 +47,105 @@ export async function finalize(ctx) {
                 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: ${prevN}→${nodeCount} [${(nodeDrift * 100).toFixed(1)}%], edges: ${prevE}→${actualEdgeCount} [${(edgeDrift * 100).toFixed(1)}%], threshold: ${(driftThreshold * 100).toFixed(0)}%). Consider rebuilding with --no-incremental.`);
+                    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.`);
                 }
             }
         }
     }
-    // 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).
+    if (isFullBuild || allSymbols.size > 5) {
         try {
-            const orphaned = db
-                .prepare('SELECT COUNT(*) as c FROM embeddings WHERE node_id NOT IN (SELECT id FROM nodes)')
+            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: ${err.message}`);
+        }
+    }
+    // Skip expensive advisory queries for incremental builds — these are
+    // informational warnings that don't affect correctness and cost ~40-60ms.
+    if (!isFullBuild) {
+        debug('Finalize: skipping advisory queries (orphaned/stale embeddings, unused exports) for incremental build');
+    }
+    else {
+        // Orphaned embeddings warning
+        if (hasEmbeddings) {
+            try {
+                const orphaned = db
+                    .prepare('SELECT COUNT(*) as c FROM embeddings WHERE node_id NOT IN (SELECT id FROM nodes)')
+                    .get().c;
+                if (orphaned > 0) {
+                    warn(`${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 (orphaned > 0) {
-                warn(`${orphaned} embeddings are orphaned (nodes changed). Run "codegraph embed" to refresh.`);
+            if (unusedCount > 0) {
+                warn(`${unusedCount} exported symbol${unusedCount > 1 ? 's have' : ' has'} zero cross-file consumers. Run "codegraph exports <file> --unused" to inspect.`);
             }
         }
         catch {
-            /* ignore — embeddings table may have been dropped */
-        }
-    }
-    // Unused exports warning
-    try {
-        const unusedCount = db
-            .prepare(`SELECT COUNT(*) as c FROM nodes
-       WHERE exported = 1 AND kind != 'file'
-         AND id NOT IN (
-           SELECT DISTINCT e.target_id FROM edges e
-           JOIN nodes caller ON e.source_id = caller.id
-           JOIN nodes target ON e.target_id = target.id
-           WHERE e.kind = 'calls' AND caller.file != target.file
-         )`)
-            .get().c;
-        if (unusedCount > 0) {
-            warn(`${unusedCount} exported symbol${unusedCount > 1 ? 's have' : ' has'} zero cross-file consumers. Run "codegraph exports <file> --unused" to inspect.`);
+            /* exported column may not exist on older DBs */
         }
     }
-    catch {
-        /* exported column may not exist on older DBs */
-    }
-    // Persist build metadata
-    try {
-        setBuildMeta(db, {
-            engine: ctx.engineName,
-            engine_version: ctx.engineVersion || '',
-            codegraph_version: CODEGRAPH_VERSION,
-            schema_version: String(schemaVersion),
-            built_at: new Date().toISOString(),
-            node_count: nodeCount,
-            edge_count: actualEdgeCount,
-        });
+    ctx.timing.finalizeMs = performance.now() - t0;
+    // For small incremental builds, defer db.close() to the next event loop tick.
+    // The WAL checkpoint in db.close() costs ~250ms on Windows NTFS due to fsync.
+    // Deferring lets buildGraph() return immediately; the checkpoint runs after.
+    // Skip for temp directories (tests) — they rmSync immediately after build.
+    const isTempDir = path.resolve(rootDir).startsWith(path.resolve(tmpdir()));
+    if (!isFullBuild && allSymbols.size <= 5 && !isTempDir) {
+        closeDbDeferred(db);
     }
-    catch (err) {
-        warn(`Failed to write build metadata: ${err.message}`);
+    else {
+        closeDb(db);
     }
-    closeDb(db);
     // Write journal header after successful build
     writeJournalHeader(rootDir, Date.now());
-    // Auto-registration
-    if (!opts.skipRegistry) {
+    // 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 } = await import('node:os');
         const tmpDir = path.resolve(tmpdir());
         const resolvedRoot = path.resolve(rootDir);
@@ -110,7 +154,7 @@ export async function finalize(ctx) {
         }
         else {
             try {
-                const { registerRepo } = await import('../../../../infrastructure/registry.js');
+                const { registerRepo } = (await import('../../../../infrastructure/registry.js'));
                 registerRepo(rootDir);
             }
             catch (err) {
@@ -118,6 +162,5 @@ export async function finalize(ctx) {
             }
         }
     }
-    ctx.timing.finalizeMs = performance.now() - t0;
 }
 //# sourceMappingURL=finalize.js.map

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

@@ -1,5 +1,3 @@
-/**
- * @param {import('../context.js').PipelineContext} ctx
- */
-export function insertNodes(ctx: import("../context.js").PipelineContext): Promise<void>;
+import type { PipelineContext } from '../context.js';
+export declare function insertNodes(ctx: PipelineContext): Promise<void>;
 //# sourceMappingURL=insert-nodes.d.ts.map

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.js"],"names":[],"mappings":"AA+JA;;GAEG;AACH,iCAFW,OAAO,eAAe,EAAE,eAAe,iBA0CjD"}
+{"version":3,"file":"insert-nodes.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/insert-nodes.ts"],"names":[],"mappings":"AAeA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA+MrD,wBAAsB,WAAW,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAuCrE"}

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

@@ -11,6 +11,7 @@ import { batchInsertEdges, batchInsertNodes, fileHash, fileStat, readFileSafe, }
 // ── Phase 1: Insert file nodes, definitions, exports ────────────────────
 function insertDefinitionsAndExports(db, allSymbols) {
     const phase1Rows = [];
+    const exportKeys = [];
     for (const [relPath, symbols] of allSymbols) {
         phase1Rows.push([relPath, 'file', relPath, 0, null, null, null, null, null]);
         for (const def of symbols.definitions) {
@@ -30,32 +31,55 @@ function insertDefinitionsAndExports(db, allSymbols) {
         }
         for (const exp of symbols.exports) {
             phase1Rows.push([exp.name, exp.kind, relPath, exp.line, null, null, exp.name, null, null]);
+            exportKeys.push([exp.name, exp.kind, relPath, exp.line]);
         }
     }
     batchInsertNodes(db, phase1Rows);
-    // Mark exported symbols
-    const markExported = db.prepare('UPDATE nodes SET exported = 1 WHERE name = ? AND kind = ? AND file = ? AND line = ?');
-    for (const [relPath, symbols] of allSymbols) {
-        for (const exp of symbols.exports) {
-            markExported.run(exp.name, exp.kind, relPath, exp.line);
+    // Mark exported symbols in batches (cache prepared statements by chunk size)
+    if (exportKeys.length > 0) {
+        const EXPORT_CHUNK = 500;
+        const exportStmtCache = new Map();
+        for (let i = 0; i < exportKeys.length; i += EXPORT_CHUNK) {
+            const end = Math.min(i + EXPORT_CHUNK, exportKeys.length);
+            const chunkSize = end - i;
+            let updateStmt = exportStmtCache.get(chunkSize);
+            if (!updateStmt) {
+                const conditions = Array.from({ length: chunkSize }, () => '(name = ? AND kind = ? AND file = ? AND line = ?)').join(' OR ');
+                updateStmt = db.prepare(`UPDATE nodes SET exported = 1 WHERE ${conditions}`);
+                exportStmtCache.set(chunkSize, updateStmt);
+            }
+            const vals = [];
+            for (let j = i; j < end; j++) {
+                const k = exportKeys[j];
+                vals.push(k[0], k[1], k[2], k[3]);
+            }
+            updateStmt.run(...vals);
         }
     }
 }
-// ── Phase 2: Insert children (needs parent IDs) ────────────────────────
-function insertChildren(db, allSymbols) {
+// ── Phase 2+3: Insert children and containment edges (two nodeIdMap passes) ──
+function insertChildrenAndEdges(db, allSymbols) {
     const childRows = [];
+    const edgeRows = [];
     for (const [relPath, symbols] of allSymbols) {
+        // First pass: collect file→def edges and child rows
         const nodeIdMap = new Map();
         for (const row of bulkNodeIdsByFile(db, relPath)) {
             nodeIdMap.set(`${row.name}|${row.kind}|${row.line}`, row.id);
         }
+        const fileId = nodeIdMap.get(`${relPath}|file|0`);
         for (const def of symbols.definitions) {
+            const defId = nodeIdMap.get(`${def.name}|${def.kind}|${def.line}`);
+            // Containment edge: file -> definition
+            if (fileId && defId) {
+                edgeRows.push([fileId, defId, 'contains', 1.0, 0]);
+            }
             if (!def.children?.length)
                 continue;
-            const defId = nodeIdMap.get(`${def.name}|${def.kind}|${def.line}`);
             if (!defId)
                 continue;
             for (const child of def.children) {
+                // Child node
                 const qualifiedName = `${def.name}.${child.name}`;
                 childRows.push([
                     child.name,
@@ -71,30 +95,26 @@ function insertChildren(db, allSymbols) {
             }
         }
     }
+    // Insert children first (so they exist for edge lookup)
     batchInsertNodes(db, childRows);
-}
-// ── Phase 3: Insert containment + parameter_of edges ────────────────────
-function insertContainmentEdges(db, allSymbols) {
-    const edgeRows = [];
+    // Now re-fetch IDs to include newly-inserted children, then add child edges
     for (const [relPath, symbols] of allSymbols) {
         const nodeIdMap = new Map();
         for (const row of bulkNodeIdsByFile(db, relPath)) {
             nodeIdMap.set(`${row.name}|${row.kind}|${row.line}`, row.id);
         }
-        const fileId = nodeIdMap.get(`${relPath}|file|0`);
         for (const def of symbols.definitions) {
+            if (!def.children?.length)
+                continue;
             const defId = nodeIdMap.get(`${def.name}|${def.kind}|${def.line}`);
-            if (fileId && defId) {
-                edgeRows.push([fileId, defId, 'contains', 1.0, 0]);
-            }
-            if (def.children?.length && defId) {
-                for (const child of def.children) {
-                    const childId = nodeIdMap.get(`${child.name}|${child.kind}|${child.line}`);
-                    if (childId) {
-                        edgeRows.push([defId, childId, 'contains', 1.0, 0]);
-                        if (child.kind === 'parameter') {
-                            edgeRows.push([childId, defId, 'parameter_of', 1.0, 0]);
-                        }
+            if (!defId)
+                continue;
+            for (const child of def.children) {
+                const childId = nodeIdMap.get(`${child.name}|${child.kind}|${child.line}`);
+                if (childId) {
+                    edgeRows.push([defId, childId, 'contains', 1.0, 0]);
+                    if (child.kind === 'parameter') {
+                        edgeRows.push([childId, defId, 'parameter_of', 1.0, 0]);
                     }
                 }
             }
@@ -112,9 +132,17 @@ function updateFileHashes(_db, allSymbols, precomputedData, metadataUpdates, roo
             // no-op: file unchanged, hash already correct
         }
         else if (precomputed?.hash) {
-            const stat = precomputed.stat || fileStat(path.join(rootDir, relPath));
-            const mtime = stat ? Math.floor(stat.mtimeMs) : 0;
-            const size = stat ? stat.size : 0;
+            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;
+            }
             upsertHash.run(relPath, precomputed.hash, mtime, size);
         }
         else {
@@ -136,15 +164,12 @@ function updateFileHashes(_db, allSymbols, precomputedData, metadataUpdates, roo
     }
     // Also update metadata-only entries (self-heal mtime/size without re-parse)
     for (const item of metadataUpdates) {
-        const mtime = item.stat ? Math.floor(item.stat.mtimeMs) : 0;
+        const mtime = item.stat ? Math.floor(item.stat.mtime) : 0;
         const size = item.stat ? item.stat.size : 0;
         upsertHash.run(item.relPath, item.hash, mtime, size);
     }
 }
 // ── Main entry point ────────────────────────────────────────────────────
-/**
- * @param {import('../context.js').PipelineContext} ctx
- */
 export async function insertNodes(ctx) {
     const { db, allSymbols, filesToParse, metadataUpdates, rootDir, removed } = ctx;
     const precomputedData = new Map();
@@ -165,8 +190,7 @@ export async function insertNodes(ctx) {
     }
     const insertAll = db.transaction(() => {
         insertDefinitionsAndExports(db, allSymbols);
-        insertChildren(db, allSymbols);
-        insertContainmentEdges(db, allSymbols);
+        insertChildrenAndEdges(db, allSymbols);
         updateFileHashes(db, allSymbols, precomputedData, metadataUpdates, rootDir, upsertHash);
     });
     const t0 = performance.now();

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

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

@@ -1,5 +1,3 @@
-/**
- * @param {import('../context.js').PipelineContext} ctx
- */
-export function parseFiles(ctx: import("../context.js").PipelineContext): Promise<void>;
+import type { PipelineContext } from '../context.js';
+export declare function parseFiles(ctx: PipelineContext): Promise<void>;
 //# sourceMappingURL=parse-files.d.ts.map

package/dist/domain/graph/builder/stages/parse-files.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"parse-files.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/parse-files.js"],"names":[],"mappings":"AAUA;;GAEG;AACH,gCAFW,OAAO,eAAe,EAAE,eAAe,iBAgBjD"}
+{"version":3,"file":"parse-files.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/parse-files.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAErD,wBAAsB,UAAU,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAcpE"}

package/dist/domain/graph/builder/stages/parse-files.js

@@ -7,9 +7,6 @@
 import { performance } from 'node:perf_hooks';
 import { info } from '../../../../infrastructure/logger.js';
 import { parseFilesAuto } from '../../../parser.js';
-/**
- * @param {import('../context.js').PipelineContext} ctx
- */
 export async function parseFiles(ctx) {
     const { allFiles, parseChanges, isFullBuild, engineOpts, rootDir } = ctx;
     ctx.filesToParse = isFullBuild ? allFiles.map((f) => ({ file: f })) : parseChanges;

package/dist/domain/graph/builder/stages/parse-files.js.map

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

@@ -1,18 +1,6 @@
-/**
- * @param {import('../context.js').PipelineContext} ctx
- */
-export function resolveImports(ctx: import("../context.js").PipelineContext): Promise<void>;
-/**
- * Resolve an import source, preferring batch results.
- * Exported so other stages (build-edges) can reuse it.
- */
-export function getResolved(ctx: any, absFile: any, importSource: any): any;
-/**
- * Check if a file is a barrel (re-export hub).
- */
-export function isBarrelFile(ctx: any, relPath: any): boolean;
-/**
- * Resolve a symbol through barrel re-export chains.
- */
-export function resolveBarrelExport(ctx: any, barrelPath: any, symbolName: any, visited?: Set<any>): any;
+import type { PipelineContext } from '../context.js';
+export declare function resolveImports(ctx: PipelineContext): Promise<void>;
+export declare function getResolved(ctx: PipelineContext, absFile: string, importSource: string): string;
+export declare function isBarrelFile(ctx: PipelineContext, relPath: string): boolean;
+export declare function resolveBarrelExport(ctx: PipelineContext, barrelPath: string, symbolName: string, visited?: Set<string>): string | null;
 //# sourceMappingURL=resolve-imports.d.ts.map

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

@@ -1 +1 @@
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+{"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"}