fix+perf: dogfood fixes 9.1-9.4 and sub-100ms incremental rebuilds (#640)

* fix: db version warning, barrel export tracing, quieter tsconfig, Set compat

9.1 — Warn on graph load when DB was built with a different codegraph
version. The check runs once per process in openReadonlyOrFail() and
suggests `build --no-incremental`.

9.2 — Barrel-only files now emit reexport edges during build. Previously
the entire file was skipped in buildImportEdges; now only non-reexport
imports are skipped, so `codegraph exports` can follow re-export chains.

9.3 — Demote "Failed to parse tsconfig.json" from warn to debug level
so it no longer clutters every build output.

9.4 — Document EXTENSIONS/IGNORE_DIRS Array→Set breaking change in
CHANGELOG. Add .toArray() convenience method and export ArrayCompatSet
type for consumers migrating from the pre-3.4 array API.

* docs: soften EXTENSIONS/IGNORE_DIRS changelog wording

* fix: address review feedback — version check, Set mutation, barrel edge duplication (#634)

- Move _versionWarned flag outside mismatch conditional to avoid
  redundant build_meta queries when versions match.
- Wrap SUPPORTED_EXTENSIONS in new Set() to avoid mutating the
  sibling module's export.
- Delete outgoing edges for barrel-only files before re-adding them
  to fileSymbols during incremental builds, preventing duplicate
  reexport edges.

* refactor: replace vendor.d.ts with @types/better-sqlite3

Delete the 39-LOC manual ambient type declarations for better-sqlite3
and use the community @types/better-sqlite3 package instead. The vendor
file was a migration-era shim (allowJs is long gone from tsconfig).

- Replace all BetterSqlite3.Database → BetterSqlite3Database (types.ts)
- Replace all BetterSqlite3.Statement → SqliteStatement (types.ts)
- Simplify constructor casts in connection.ts, branch-compare.ts,
  snapshot.ts (no longer needed with proper @types)
- Clean up watcher.ts double-cast and info.ts @ts-expect-error
- Widen transaction() return type for @types compatibility

* fix: address Greptile review feedback

- Restore warn level for tsconfig/jsconfig parse errors (P1: was
  incorrectly downgraded to debug; ENOENT is already guarded by
  existsSync before the try block)
- Simplify openReadonlyOrFail constructor cast to match openDb pattern (P2)
- Use Object.assign in withArrayCompat instead of cast-then-mutate (P2)
- Remove unused BetterSqlite3Database import from branch-compare.ts
- Remove stale biome-ignore suppression from snapshot.ts

* fix: preserve transaction argument types via inline inference (#640)

* perf: sub-100ms 1-file incremental rebuilds (466ms → 78-90ms)

Four optimizations for small incremental builds (≤5 changed files):

1. Scope barrel re-parsing to related barrels only (resolve-imports.ts)
   Instead of parsing ALL barrel files one-by-one (~93ms), only re-parse
   barrels imported by or re-exporting from changed files, batch-parsed
   in one call (~11ms).

2. Fast-path structure metrics (build-structure.ts)
   For ≤5 changed files on large codebases (>20 files), use targeted
   per-file SQL queries (~2ms) instead of loading ALL definitions from
   DB and recomputing ALL metrics (~35ms).

3. Skip unnecessary finalize work (finalize.ts)
   - Skip setBuildMeta writes for ≤5 files (avoids WAL transaction)
   - Skip drift detection for ≤3 files
   - Skip auto-registration dynamic import for incremental builds
   - Move timing measurement before db.close()

4. Deferred db.close() for small incremental builds (connection.ts)
   WAL checkpoint in db.close() costs ~250ms on Windows NTFS. Defer to
   next event loop tick so buildGraph() returns immediately. Includes
   flushDeferredClose() for test compatibility and auto-flush on openDb().

Author: carlos-alm

package-lock.json

@@ -94,6 +94,7 @@
     "@commitlint/config-conventional": "^20.0",
     "@huggingface/transformers": "^3.8.1",
     "@tree-sitter-grammars/tree-sitter-hcl": "^1.2.0",
+    "@types/better-sqlite3": "^7.6.13",
     "@vitest/coverage-v8": "^4.0.18",
     "commit-and-tag-version": "^12.5",
     "husky": "^9.1",

package.json

@@ -43,7 +43,6 @@ export const command: CommandDefinition = {
       const dbPath = findDbPath();
       const fs = await import('node:fs');
       if (fs.existsSync(dbPath)) {
-        // @ts-expect-error -- better-sqlite3 default export typing
         const db = new Database(dbPath, { readonly: true });
         const buildEngine = getBuildMeta(db, 'engine');
         const buildVersion = getBuildMeta(db, 'codegraph_version');

src/cli/commands/info.ts

@@ -1,11 +1,11 @@
-import type Database from 'better-sqlite3';
 import { openReadonlyOrFail } from '../../db/index.js';
+import type { BetterSqlite3Database } from '../../types.js';
 
 /**
  * Open the graph database in readonly mode with a clean close() handle.
  */
 export function openGraph(opts: { db?: string } = {}): {
-  db: Database.Database;
+  db: BetterSqlite3Database;
   close: () => void;
 } {
   const db = openReadonlyOrFail(opts.db);

src/cli/shared/open-graph.ts

@@ -143,16 +143,12 @@ function isSameDirectory(a: string, b: string): boolean {
 }
 
 export function openDb(dbPath: string): LockedDatabase {
+  // Flush any deferred DB close from a previous build (avoids WAL contention)
+  flushDeferredClose();
   const dir = path.dirname(dbPath);
   if (!fs.existsSync(dir)) fs.mkdirSync(dir, { recursive: true });
   acquireAdvisoryLock(dbPath);
-  // vendor.d.ts declares Database as a callable; cast through unknown for construct usage
-  const db = new (
-    Database as unknown as new (
-      path: string,
-      opts?: Record<string, unknown>,
-    ) => LockedDatabase
-  )(dbPath);
+  const db = new Database(dbPath) as unknown as LockedDatabase;
   db.pragma('journal_mode = WAL');
   db.pragma('busy_timeout = 5000');
   db.__lockPath = `${dbPath}.lock`;
@@ -164,6 +160,54 @@ export function closeDb(db: LockedDatabase): void {
   if (db.__lockPath) releaseAdvisoryLock(db.__lockPath);
 }
 
+/** Pending deferred-close DB handles (not yet closed). */
+const _deferredDbs: LockedDatabase[] = [];
+
+/**
+ * Synchronously close any DB handles queued by `closeDbDeferred()`.
+ * Call before deleting DB files or in test teardown to avoid EBUSY on Windows.
+ */
+export function flushDeferredClose(): void {
+  while (_deferredDbs.length > 0) {
+    const db = _deferredDbs.pop()!;
+    try {
+      db.close();
+    } catch {
+      /* ignore — handle may already be closed */
+    }
+  }
+}
+
+/**
+ * Schedule DB close on the next event loop tick. Useful for incremental
+ * builds where the WAL checkpoint in db.close() is expensive (~250ms on
+ * Windows) and doesn't need to block the caller.
+ *
+ * The advisory lock is released immediately so subsequent opens succeed.
+ * The actual handle close (+ WAL checkpoint) happens asynchronously.
+ * Call `flushDeferredClose()` before deleting the DB file.
+ */
+export function closeDbDeferred(db: LockedDatabase): void {
+  // Release the advisory lock immediately so the next open can proceed
+  if (db.__lockPath) {
+    releaseAdvisoryLock(db.__lockPath);
+    db.__lockPath = undefined;
+  }
+  _deferredDbs.push(db);
+  // Defer the expensive WAL checkpoint to after the caller returns
+  setImmediate(() => {
+    const idx = _deferredDbs.indexOf(db);
+    if (idx !== -1) {
+      _deferredDbs.splice(idx, 1);
+      try {
+        db.close();
+      } catch {
+        /* ignore — handle may already be closed by flush */
+      }
+    }
+  });
+}
+
 export function findDbPath(customPath?: string): string {
   if (customPath) return path.resolve(customPath);
   const rawCeiling = findRepoRoot();
@@ -214,12 +258,7 @@ export function openReadonlyOrFail(customPath?: string): BetterSqlite3Database {
       { file: dbPath },
     );
   }
-  const db = new (
-    Database as unknown as new (
-      path: string,
-      opts?: Record<string, unknown>,
-    ) => BetterSqlite3Database
-  )(dbPath, { readonly: true });
+  const db = new Database(dbPath, { readonly: true }) as unknown as BetterSqlite3Database;
 
   // Warn once per process if the DB was built with a different codegraph version
   if (!_versionWarned) {

src/db/connection.ts

@@ -3,8 +3,10 @@
 export type { LockedDatabase } from './connection.js';
 export {
   closeDb,
+  closeDbDeferred,
   findDbPath,
   findRepoRoot,
+  flushDeferredClose,
   openDb,
   openReadonlyOrFail,
   openRepo,

src/db/index.ts

@@ -4,8 +4,8 @@
  * Each stage reads what it needs and writes what it produces.
  * This replaces the closure-captured locals in the old monolithic buildGraph().
  */
-import type BetterSqlite3 from 'better-sqlite3';
 import type {
+  BetterSqlite3Database,
   BuildGraphOpts,
   CodegraphConfig,
   EngineOpts,
@@ -20,7 +20,7 @@ import type {
 export class PipelineContext {
   // ── Inputs (set during setup) ──────────────────────────────────────
   rootDir!: string;
-  db!: BetterSqlite3.Database;
+  db!: BetterSqlite3Database;
   dbPath!: string;
   config!: CodegraphConfig;
   opts!: BuildGraphOpts;

src/domain/graph/builder/context.ts

@@ -6,11 +6,15 @@
 import { createHash } from 'node:crypto';
 import fs from 'node:fs';
 import path from 'node:path';
-import type BetterSqlite3 from 'better-sqlite3';
 import { purgeFilesData } from '../../../db/index.js';
-import { debug, warn } from '../../../infrastructure/logger.js';
+import { warn } from '../../../infrastructure/logger.js';
 import { EXTENSIONS, IGNORE_DIRS } from '../../../shared/constants.js';
-import type { BetterSqlite3Database, CodegraphConfig, PathAliases } from '../../../types.js';
+import type {
+  BetterSqlite3Database,
+  CodegraphConfig,
+  PathAliases,
+  SqliteStatement,
+} from '../../../types.js';
 
 export const BUILTIN_RECEIVERS: Set<string> = new Set([
   'console',
@@ -148,7 +152,7 @@ export function loadPathAliases(rootDir: string): PathAliases {
       }
       break;
     } catch (err: unknown) {
-      debug(`Failed to parse ${configName}: ${(err as Error).message}`);
+      warn(`Failed to parse ${configName}: ${(err as Error).message}`);
     }
   }
   return aliases;
@@ -198,7 +202,7 @@ export function readFileSafe(filePath: string, retries: number = 2): string {
  * Purge all graph data for the specified files.
  */
 export function purgeFilesFromGraph(
-  db: BetterSqlite3.Database,
+  db: BetterSqlite3Database,
   files: string[],
   options: Record<string, unknown> = {},
 ): void {
@@ -210,10 +214,10 @@ export function purgeFilesFromGraph(
 const BATCH_CHUNK = 500;
 
 // Statement caches keyed by chunk size — avoids recompiling for every batch.
-const nodeStmtCache = new WeakMap<BetterSqlite3.Database, Map<number, BetterSqlite3.Statement>>();
-const edgeStmtCache = new WeakMap<BetterSqlite3.Database, Map<number, BetterSqlite3.Statement>>();
+const nodeStmtCache = new WeakMap<BetterSqlite3Database, Map<number, SqliteStatement>>();
+const edgeStmtCache = new WeakMap<BetterSqlite3Database, Map<number, SqliteStatement>>();
 
-function getNodeStmt(db: BetterSqlite3.Database, chunkSize: number): BetterSqlite3.Statement {
+function getNodeStmt(db: BetterSqlite3Database, chunkSize: number): SqliteStatement {
   let cache = nodeStmtCache.get(db);
   if (!cache) {
     cache = new Map();
@@ -231,7 +235,7 @@ function getNodeStmt(db: BetterSqlite3.Database, chunkSize: number): BetterSqlit
   return stmt;
 }
 
-function getEdgeStmt(db: BetterSqlite3.Database, chunkSize: number): BetterSqlite3.Statement {
+function getEdgeStmt(db: BetterSqlite3Database, chunkSize: number): SqliteStatement {
   let cache = edgeStmtCache.get(db);
   if (!cache) {
     cache = new Map();
@@ -253,7 +257,7 @@ function getEdgeStmt(db: BetterSqlite3.Database, chunkSize: number): BetterSqlit
  * Batch-insert node rows via multi-value INSERT statements.
  * Each row: [name, kind, file, line, end_line, parent_id, qualified_name, scope, visibility]
  */
-export function batchInsertNodes(db: BetterSqlite3.Database, rows: unknown[][]): void {
+export function batchInsertNodes(db: BetterSqlite3Database, rows: unknown[][]): void {
   if (!rows.length) return;
   for (let i = 0; i < rows.length; i += BATCH_CHUNK) {
     const end = Math.min(i + BATCH_CHUNK, rows.length);
@@ -272,7 +276,7 @@ export function batchInsertNodes(db: BetterSqlite3.Database, rows: unknown[][]):
  * Batch-insert edge rows via multi-value INSERT statements.
  * Each row: [source_id, target_id, kind, confidence, dynamic]
  */
-export function batchInsertEdges(db: BetterSqlite3.Database, rows: unknown[][]): void {
+export function batchInsertEdges(db: BetterSqlite3Database, rows: unknown[][]): void {
   if (!rows.length) return;
   for (let i = 0; i < rows.length; i += BATCH_CHUNK) {
     const end = Math.min(i + BATCH_CHUNK, rows.length);