diff --git a/README.md b/README.md
index 7c7b84a9..40e388c1 100644
--- a/README.md
+++ b/README.md
@@ -575,7 +575,8 @@ What it skips out of the box:
   [supported stack](#supported-languages) — so the graph is your code, not
   third-party noise. This holds even with no `.gitignore`.
 - **Anything in your `.gitignore`** — honored in git repos via git, and in
-  non-git projects by reading `.gitignore` directly (root and nested).
+  non-git projects by reading `.gitignore` directly (root and nested). Add a
+  local `.ignore` next to `.gitignore` when you need CodeGraph-only overrides.
 - **Files larger than 1 MB** — generated bundles, minified JS, vendored blobs.
 
 To keep something else out, add it to `.gitignore`. To pull a default-excluded
@@ -584,6 +585,11 @@ add a negation — `!vendor/`. The defaults apply uniformly, so committing a
 dependency or build directory doesn't force it into the graph; the `.gitignore`
 negation is the explicit opt-in.
 
+If a path must stay gitignored but should still be indexed locally, put the
+negation in `.ignore` instead. For example, `.gitignore` can keep `customer/`
+out of git while `.ignore` contains `!customer/` so CodeGraph indexes that
+customer source without changing repository semantics.
+
 ## Supported Platforms
 
 Every release ships a self-contained build (bundled Node runtime — nothing to
diff --git a/__tests__/extraction.test.ts b/__tests__/extraction.test.ts
index 6d9af606..c98b0a0c 100644
--- a/__tests__/extraction.test.ts
+++ b/__tests__/extraction.test.ts
@@ -4955,6 +4955,26 @@ describe('Directory Exclusion', () => {
     expect(files.every((f) => !f.includes('node_modules'))).toBe(true);
   });
 
+  it('should allow a root .ignore negation to re-include a gitignored directory', async () => {
+    const { execFileSync } = await import('child_process');
+    const git = (cwd: string, ...args: string[]) =>
+      execFileSync('git', args, { cwd, stdio: 'pipe' });
+
+    const root = path.join(tempDir, 'repo');
+    fs.mkdirSync(path.join(root, 'src'), { recursive: true });
+    fs.mkdirSync(path.join(root, 'customer'), { recursive: true });
+    git(root, 'init', '-q');
+    fs.writeFileSync(path.join(root, 'src', 'index.ts'), 'export const x = 1;');
+    fs.writeFileSync(path.join(root, 'customer', 'custom.ts'), 'export const custom = 1;');
+    fs.writeFileSync(path.join(root, '.gitignore'), 'customer/\n');
+    fs.writeFileSync(path.join(root, '.ignore'), '!customer/\n');
+
+    const files = scanDirectory(root);
+
+    expect(files).toContain('src/index.ts');
+    expect(files).toContain('customer/custom.ts');
+  });
+
   it('should apply a nested .gitignore only to its own subtree', () => {
     const appSrc = path.join(tempDir, 'app', 'src');
     fs.mkdirSync(appSrc, { recursive: true });
diff --git a/__tests__/watcher.test.ts b/__tests__/watcher.test.ts
index b372fc3d..f6c32fa6 100644
--- a/__tests__/watcher.test.ts
+++ b/__tests__/watcher.test.ts
@@ -203,6 +203,24 @@ describe('FileWatcher', () => {
 
       watcher.stop();
     });
+
+    it('should sync a gitignored source file re-included by .ignore', async () => {
+      fs.writeFileSync(path.join(testDir, '.gitignore'), 'customer/\n');
+      fs.writeFileSync(path.join(testDir, '.ignore'), '!customer/\n');
+      fs.mkdirSync(path.join(testDir, 'customer'), { recursive: true });
+      fs.writeFileSync(path.join(testDir, 'customer', 'custom.ts'), 'export const custom = 1;');
+
+      const syncFn = vi.fn().mockResolvedValue({ filesChanged: 0, durationMs: 0 });
+      const watcher = newWatcher(syncFn, { debounceMs: 200 });
+      watcher.start();
+      await watcher.waitUntilReady();
+
+      __emitWatchEventForTests(testDir, 'customer/custom.ts');
+      await waitFor(() => syncFn.mock.calls.length > 0);
+      expect(syncFn).toHaveBeenCalled();
+
+      watcher.stop();
+    });
   });
 
   describe('pending file tracking (#403)', () => {
diff --git a/src/extraction/index.ts b/src/extraction/index.ts
index 36569258..39f8409c 100644
--- a/src/extraction/index.ts
+++ b/src/extraction/index.ts
@@ -161,7 +161,8 @@ const DEFAULT_IGNORE_PATTERNS: string[] = [
 
 /**
  * An `ignore` matcher seeded with the built-in defaults, merged with the project's
- * root .gitignore so a negation there (e.g. `!vendor/`) overrides a default. Shared
+ * root .gitignore and then root .ignore so a negation there (e.g. `!vendor/`)
+ * overrides an earlier exclusion. Shared
  * by both enumeration paths so behavior is identical with or without git — and so
  * the defaults apply to tracked files too (committing a dependency dir doesn't make
  * it project code; the explicit `.gitignore` negation is the only opt-in).
@@ -171,8 +172,10 @@ export function buildDefaultIgnore(rootDir: string): Ignore {
   try {
     const rootGitignore = path.join(rootDir, '.gitignore');
     if (fs.existsSync(rootGitignore)) ig.add(fs.readFileSync(rootGitignore, 'utf-8'));
+    const rootIgnore = path.join(rootDir, '.ignore');
+    if (fs.existsSync(rootIgnore)) ig.add(fs.readFileSync(rootIgnore, 'utf-8'));
   } catch {
-    // Unreadable root .gitignore — the built-in defaults still apply.
+    // Unreadable root ignore files — the built-in defaults still apply.
   }
   return ig;
 }
@@ -235,6 +238,8 @@ function collectGitFiles(repoDir: string, prefix: string, files: Set<string>): v
  */
 function getGitVisibleFiles(rootDir: string): Set<string> | null {
   try {
+    if (fs.existsSync(path.join(rootDir, '.ignore'))) return null;
+
     // Check if the project directory is gitignored by a parent repo.
     // When rootDir lives inside a parent git repo that ignores it,
     // `git ls-files` returns nothing — fall back to filesystem walk.
@@ -393,8 +398,8 @@ function scanDirectoryWalk(
   let count = 0;
   const visitedDirs = new Set<string>();
 
-  // A .gitignore matcher scoped to the directory that declared it. Patterns in
-  // a nested .gitignore are relative to that directory, so we keep the dir
+  // A matcher scoped to the directory that declared ignore files. Patterns in
+  // nested .gitignore/.ignore files are relative to that directory, so we keep the dir
   // alongside the matcher and test paths relative to it — mirroring how git
   // applies .gitignore files at every level.
   interface ScopedIgnore {
@@ -404,12 +409,20 @@ function scanDirectoryWalk(
 
   const loadIgnore = (dir: string): ScopedIgnore | null => {
     try {
+      const patterns: string[] = [];
       const giPath = path.join(dir, '.gitignore');
       if (fs.existsSync(giPath)) {
-        return { dir, ig: ignore().add(fs.readFileSync(giPath, 'utf-8')) };
+        patterns.push(fs.readFileSync(giPath, 'utf-8'));
+      }
+      const ignorePath = path.join(dir, '.ignore');
+      if (fs.existsSync(ignorePath)) {
+        patterns.push(fs.readFileSync(ignorePath, 'utf-8'));
+      }
+      if (patterns.length > 0) {
+        return { dir, ig: ignore().add(patterns) };
       }
     } catch {
-      // Unreadable .gitignore — treat as absent.
+      // Unreadable ignore files — treat as absent.
     }
     return null;
   };
@@ -439,9 +452,9 @@ function scanDirectoryWalk(
     }
     visitedDirs.add(realDir);
 
-    // This directory's own .gitignore (if present) applies to everything below it.
-    // The root's .gitignore is already merged into the seeded base matcher (so a
-    // negation there can override a built-in default), so skip it here.
+    // This directory's own ignore files (if present) apply to everything below it.
+    // The root ignore files are already merged into the seeded base matcher (so a
+    // negation there can override an earlier exclusion), so skip them here.
     const own = dir === rootDir ? null : loadIgnore(dir);
     const active = own ? [...matchers, own] : matchers;
 
@@ -495,8 +508,8 @@ function scanDirectoryWalk(
     }
   }
 
-  // Seed a base matcher with the built-in default ignores (merged with the root
-  // .gitignore so a negation can override). Nested .gitignores still layer per-dir.
+  // Seed a base matcher with the built-in default ignores merged with the root
+  // .gitignore/.ignore overlay. Nested ignore files still layer per-dir.
   walk(rootDir, [{ dir: rootDir, ig: buildDefaultIgnore(rootDir) }]);
   return files;
 }