diff --git a/.codegraphrc.json b/.codegraphrc.json
index ce8446627..815885b8d 100644
--- a/.codegraphrc.json
+++ b/.codegraphrc.json
@@ -1,4 +1,5 @@
 {
   "embeddings": { "model": "bge-large" },
-  "exclude": ["crates/**"]
+  "exclude": ["crates/**"],
+  "ignoreAdditionalDirs": ["crates"]
 }
diff --git a/crates/codegraph-core/src/domain/graph/builder/stages/collect_files.rs b/crates/codegraph-core/src/domain/graph/builder/stages/collect_files.rs
index 59a9e561d..cf127d92d 100644
--- a/crates/codegraph-core/src/domain/graph/builder/stages/collect_files.rs
+++ b/crates/codegraph-core/src/domain/graph/builder/stages/collect_files.rs
@@ -28,9 +28,6 @@ const DEFAULT_IGNORE_DIRS: &[&str] = &[
     "venv",
     "env",
     ".env",
-    // Rust workspace convention — contains only Rust source and NAPI-RS generated
-    // binding artifacts (index.js / index.d.ts) that produce false complexity readings.
-    "crates",
 ];
 
 /// All supported file extensions (mirrors the JS `EXTENSIONS` set).
diff --git a/src/domain/graph/builder/helpers.ts b/src/domain/graph/builder/helpers.ts
index c2f8ab0c4..1c6859667 100644
--- a/src/domain/graph/builder/helpers.ts
+++ b/src/domain/graph/builder/helpers.ts
@@ -8,7 +8,7 @@ import fs from 'node:fs';
 import path from 'node:path';
 import { purgeFilesData } from '../../../db/index.js';
 import { debug, warn } from '../../../infrastructure/logger.js';
-import { EXTENSIONS, IGNORE_DIRS, normalizePath } from '../../../shared/constants.js';
+import { buildIgnoreSet, EXTENSIONS, normalizePath } from '../../../shared/constants.js';
 import { compileGlobs, globToRegex, matchesAny } from '../../../shared/globs.js';
 import type {
   BetterSqlite3Database,
@@ -56,13 +56,12 @@ export const CHA_DISPATCH_PENALTY = 0.1;
 export const CHA_TYPED_DISPATCH_CONFIDENCE = 0.8;
 
 /** Check if a directory entry should be skipped (ignored dirs, dotfiles). */
-function shouldSkipEntry(entry: fs.Dirent, extraIgnore: Set<string> | null): boolean {
+function shouldSkipEntry(entry: fs.Dirent, ignoreSet: ReadonlySet<string>): boolean {
   if (entry.name.startsWith('.') && entry.name !== '.') {
-    if (IGNORE_DIRS.has(entry.name)) return true;
+    if (ignoreSet.has(entry.name)) return true;
     if (entry.isDirectory()) return true;
   }
-  if (IGNORE_DIRS.has(entry.name)) return true;
-  if (extraIgnore?.has(entry.name)) return true;
+  if (ignoreSet.has(entry.name)) return true;
   return false;
 }
 
@@ -140,7 +139,8 @@ interface CollectContext {
   readonly excludeRegexes: readonly RegExp[];
   readonly gitignoreRegexes: readonly RegExp[];
   readonly hasGlobFilters: boolean;
-  readonly extraIgnore: Set<string> | null;
+  /** Merged set of IGNORE_DIRS + config.ignoreDirs + config.ignoreAdditionalDirs. */
+  readonly ignoreSet: ReadonlySet<string>;
   readonly visited: Set<string>;
 }
 
@@ -193,7 +193,7 @@ function walkCollect(
 
   let hasFiles = false;
   for (const entry of entries) {
-    if (shouldSkipEntry(entry, ctx.extraIgnore)) continue;
+    if (shouldSkipEntry(entry, ctx.ignoreSet)) continue;
 
     const full = path.join(dir, entry.name);
     if (entry.isDirectory()) {
@@ -237,13 +237,18 @@ export function collectFiles(
   const includeRegexes = compileGlobs(config.include);
   const excludeRegexes = compileGlobs(config.exclude);
   const gitignoreRegexes = readGitignorePatterns(dir);
+  // Build the merged ignore set:
+  //   - config.ignoreDirs are appended to IGNORE_DIRS (existing behaviour: per-repo overrides)
+  //   - config.ignoreAdditionalDirs are also merged in on top of IGNORE_DIRS (new feature)
+  const extraDirs = [...(config.ignoreDirs ?? []), ...(config.ignoreAdditionalDirs ?? [])];
+  const ignoreSet = buildIgnoreSet(extraDirs.length ? extraDirs : undefined);
   const ctx: CollectContext = {
     rootDir: dir,
     includeRegexes,
     excludeRegexes,
     gitignoreRegexes,
     hasGlobFilters: includeRegexes.length > 0 || excludeRegexes.length > 0,
-    extraIgnore: config.ignoreDirs ? new Set(config.ignoreDirs) : null,
+    ignoreSet,
     visited: new Set(),
   };
 
diff --git a/src/domain/graph/builder/stages/native-orchestrator.ts b/src/domain/graph/builder/stages/native-orchestrator.ts
index 5b04ba39b..db92277ef 100644
--- a/src/domain/graph/builder/stages/native-orchestrator.ts
+++ b/src/domain/graph/builder/stages/native-orchestrator.ts
@@ -2105,11 +2105,9 @@ export async function tryNativeOrchestrator(
   // nodes/edges during incremental builds, so FK enforcement causes the purge
   // statements to fail silently — leaving stale nodes and edges that then get
   // duplicated when the barrel-candidate re-parse re-inserts them (issue #1644).
-  // Disabling FK before buildGraph() lets the purge succeed. FK stays OFF for
-  // the entire connection lifetime (through backfillNativeDroppedFiles and
-  // buildDataflowP4ForNative) and is restored when the connection is closed.
-  // This is intentional: call_edge_id values written by P4 are always looked up
-  // live from the edges table, so no phantom FK reference is ever produced.
+  // Disabling FK before buildGraph() lets the purge succeed; FK is restored in
+  // a finally block so post-passes (gap-repair, structure patch) retain FK protection
+  // even if buildGraph() throws.
   try {
     ctx.nativeDb.exec('PRAGMA foreign_keys = OFF');
   } catch {
diff --git a/src/domain/graph/watcher.ts b/src/domain/graph/watcher.ts
index f0ef8028c..d922307e6 100644
--- a/src/domain/graph/watcher.ts
+++ b/src/domain/graph/watcher.ts
@@ -1,17 +1,18 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import { closeDb, getNodeId as getNodeIdQuery, initSchema, openDb } from '../../db/index.js';
+import { loadConfig } from '../../infrastructure/config.js';
 import { debug, info, warn } from '../../infrastructure/logger.js';
-import { isSupportedFile, normalizePath, shouldIgnore } from '../../shared/constants.js';
+import { buildIgnoreSet, isSupportedFile, normalizePath } from '../../shared/constants.js';
 import { DbError } from '../../shared/errors.js';
 import { createParseTreeCache, getActiveEngine } from '../parser.js';
 import { type IncrementalStmts, rebuildFile } from './builder/incremental.js';
 import { appendChangeEvents, buildChangeEvent, diffSymbols } from './change-journal.js';
 import { appendJournalEntriesAndStampHeader } from './journal.js';
 
-function shouldIgnorePath(filePath: string): boolean {
+function shouldIgnorePath(filePath: string, ignoreSet: ReadonlySet<string>): boolean {
   const parts = filePath.split(path.sep);
-  return parts.some((p) => shouldIgnore(p));
+  return parts.some((p) => ignoreSet.has(p) || p.startsWith('.'));
 }
 
 /** Prepare all SQL statements needed by the watcher's incremental rebuild. */
@@ -139,7 +140,7 @@ function logRebuildResults(updates: RebuildResult[]): void {
 }
 
 /** Recursively collect tracked source files for stat-based polling. */
-function collectTrackedFiles(dir: string, result: string[]): void {
+function collectTrackedFiles(dir: string, result: string[], ignoreSet: ReadonlySet<string>): void {
   let entries: fs.Dirent[];
   try {
     entries = fs.readdirSync(dir, { withFileTypes: true });
@@ -148,10 +149,10 @@ function collectTrackedFiles(dir: string, result: string[]): void {
     return;
   }
   for (const entry of entries) {
-    if (shouldIgnore(entry.name)) continue;
+    if (ignoreSet.has(entry.name) || entry.name.startsWith('.')) continue;
     const full = path.join(dir, entry.name);
     if (entry.isDirectory()) {
-      collectTrackedFiles(full, result);
+      collectTrackedFiles(full, result, ignoreSet);
     } else if (isSupportedFile(entry.name)) {
       result.push(full);
     }
@@ -168,6 +169,8 @@ interface WatcherContext {
   pending: Set<string>;
   timer: ReturnType<typeof setTimeout> | null;
   debounceMs: number;
+  /** Merged ignore set from IGNORE_DIRS + config.ignoreDirs + config.ignoreAdditionalDirs. */
+  ignoreSet: ReadonlySet<string>;
 }
 
 /** Initialize DB, engine, cache, and statements for watch mode. */
@@ -177,6 +180,12 @@ function setupWatcher(rootDir: string, opts: { engine?: string; dbPath?: string
     throw new DbError('No graph.db found. Run `codegraph build` first.', { file: dbPath });
   }
 
+  // Load repo config so ignoreDirs and ignoreAdditionalDirs are respected by
+  // the watcher the same way they are by collectFiles in the batch build path.
+  const config = loadConfig(rootDir);
+  const extraDirs = [...(config.ignoreDirs ?? []), ...(config.ignoreAdditionalDirs ?? [])];
+  const ignoreSet = buildIgnoreSet(extraDirs.length ? extraDirs : undefined);
+
   const db = openDb(dbPath);
   initSchema(db);
   const engineOpts: import('../../types.js').EngineOpts = {
@@ -205,6 +214,7 @@ function setupWatcher(rootDir: string, opts: { engine?: string; dbPath?: string
     pending: new Set<string>(),
     timer: null,
     debounceMs: 300,
+    ignoreSet,
   };
 }
 
@@ -223,7 +233,7 @@ function startPollingWatcher(ctx: WatcherContext, pollIntervalMs: number): () =>
   const mtimeMap = new Map<string, number>();
 
   const initial: string[] = [];
-  collectTrackedFiles(ctx.rootDir, initial);
+  collectTrackedFiles(ctx.rootDir, initial, ctx.ignoreSet);
   for (const f of initial) {
     try {
       mtimeMap.set(f, fs.statSync(f).mtimeMs);
@@ -235,7 +245,7 @@ function startPollingWatcher(ctx: WatcherContext, pollIntervalMs: number): () =>
 
   const pollTimer = setInterval(() => {
     const current: string[] = [];
-    collectTrackedFiles(ctx.rootDir, current);
+    collectTrackedFiles(ctx.rootDir, current, ctx.ignoreSet);
     const currentSet = new Set(current);
 
     for (const f of current) {
@@ -270,7 +280,7 @@ function startPollingWatcher(ctx: WatcherContext, pollIntervalMs: number): () =>
 function startNativeWatcher(ctx: WatcherContext): () => void {
   const watcher = fs.watch(ctx.rootDir, { recursive: true }, (_eventType, filename) => {
     if (!filename) return;
-    if (shouldIgnorePath(filename)) return;
+    if (shouldIgnorePath(filename, ctx.ignoreSet)) return;
     if (!isSupportedFile(filename)) return;
 
     ctx.pending.add(path.join(ctx.rootDir, filename));
diff --git a/src/infrastructure/config.ts b/src/infrastructure/config.ts
index 519f17570..1e5492ee9 100644
--- a/src/infrastructure/config.ts
+++ b/src/infrastructure/config.ts
@@ -21,6 +21,7 @@ export const DEFAULTS = {
   include: [] as string[],
   exclude: [] as string[],
   ignoreDirs: [] as string[],
+  ignoreAdditionalDirs: [] as string[],
   extensions: [] as string[],
   aliases: {} as Record<string, string>,
   build: {
@@ -452,6 +453,7 @@ const BUILD_HASH_KEYS: ReadonlyArray<keyof CodegraphConfig> = [
   'include',
   'exclude',
   'ignoreDirs',
+  'ignoreAdditionalDirs',
   'extensions',
   'aliases',
   'build',
diff --git a/src/shared/constants.ts b/src/shared/constants.ts
index af702f2d9..9dc88056e 100644
--- a/src/shared/constants.ts
+++ b/src/shared/constants.ts
@@ -34,6 +34,15 @@ export const IGNORE_DIRS: ArrayCompatSet<string> = withArrayCompat(
   ]),
 );
 
+/**
+ * Merge the global IGNORE_DIRS set with a per-repo additional list from config.
+ * Returns a new Set — does not mutate IGNORE_DIRS.
+ */
+export function buildIgnoreSet(additionalDirs?: string[]): ReadonlySet<string> {
+  if (!additionalDirs || additionalDirs.length === 0) return IGNORE_DIRS;
+  return new Set([...IGNORE_DIRS, ...additionalDirs]);
+}
+
 export const EXTENSIONS: ArrayCompatSet<string> = withArrayCompat(new Set(SUPPORTED_EXTENSIONS));
 
 /**
diff --git a/src/types.ts b/src/types.ts
index fa2890b6b..08910e9cc 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -1351,6 +1351,8 @@ export interface CodegraphConfig {
   include: string[];
   exclude: string[];
   ignoreDirs: string[];
+  /** Additional directory names to ignore on top of the built-in IGNORE_DIRS set. */
+  ignoreAdditionalDirs: string[];
   extensions: string[];
   aliases: Record<string, unknown>;
 
diff --git a/tests/unit/builder.test.ts b/tests/unit/builder.test.ts
index a7140e2ae..a619e969e 100644
--- a/tests/unit/builder.test.ts
+++ b/tests/unit/builder.test.ts
@@ -105,6 +105,22 @@ describe('collectFiles', () => {
     expect(basenames).toContain('app.js');
   });
 
+  it('respects config.ignoreAdditionalDirs', () => {
+    const files = collectFiles(tmpDir, [], { ignoreAdditionalDirs: ['lib'] });
+    const basenames = files.map((f) => path.basename(f));
+    expect(basenames).not.toContain('helper.py');
+    // src files still present
+    expect(basenames).toContain('app.js');
+  });
+
+  it('merges ignoreAdditionalDirs with ignoreDirs when both are set', () => {
+    // ignoreDirs excludes 'lib', ignoreAdditionalDirs excludes 'src'
+    const files = collectFiles(tmpDir, [], { ignoreDirs: ['lib'], ignoreAdditionalDirs: ['src'] });
+    const basenames = files.map((f) => path.basename(f));
+    expect(basenames).not.toContain('helper.py'); // lib excluded
+    expect(basenames).not.toContain('app.js'); // src excluded
+  });
+
   it('returns empty array for non-existent directory (graceful)', () => {
     const files = collectFiles(path.join(tmpDir, 'does-not-exist'));
     expect(files).toEqual([]);
diff --git a/tests/unit/constants.test.ts b/tests/unit/constants.test.ts
index 81ed4dbaa..fcce3bc84 100644
--- a/tests/unit/constants.test.ts
+++ b/tests/unit/constants.test.ts
@@ -5,6 +5,7 @@
 import path from 'node:path';
 import { describe, expect, it } from 'vitest';
 import {
+  buildIgnoreSet,
   EXTENSIONS,
   IGNORE_DIRS,
   isSupportedFile,
@@ -49,6 +50,36 @@ describe('IGNORE_DIRS', () => {
       expect(IGNORE_DIRS.has(dir)).toBe(true);
     }
   });
+
+  it('does not contain crates (repo-specific dirs belong in ignoreAdditionalDirs config)', () => {
+    expect(IGNORE_DIRS.has('crates')).toBe(false);
+  });
+});
+
+describe('buildIgnoreSet', () => {
+  it('returns IGNORE_DIRS when no additional dirs provided', () => {
+    const result = buildIgnoreSet();
+    expect(result).toBe(IGNORE_DIRS);
+  });
+
+  it('returns IGNORE_DIRS when empty array provided', () => {
+    const result = buildIgnoreSet([]);
+    expect(result).toBe(IGNORE_DIRS);
+  });
+
+  it('merges additional dirs on top of IGNORE_DIRS', () => {
+    const result = buildIgnoreSet(['crates', 'generated']);
+    expect(result.has('node_modules')).toBe(true); // from IGNORE_DIRS
+    expect(result.has('crates')).toBe(true); // additional
+    expect(result.has('generated')).toBe(true); // additional
+  });
+
+  it('does not mutate IGNORE_DIRS', () => {
+    const before = new Set(IGNORE_DIRS);
+    buildIgnoreSet(['crates']);
+    expect(IGNORE_DIRS.size).toBe(before.size);
+    expect(IGNORE_DIRS.has('crates')).toBe(false);
+  });
 });
 
 describe('shouldIgnore', () => {