diff --git a/src/core/file-watcher.ts b/src/core/file-watcher.ts
index 6abc3ba..4687466 100644
--- a/src/core/file-watcher.ts
+++ b/src/core/file-watcher.ts
@@ -1,4 +1,6 @@
 import chokidar from 'chokidar';
+import path from 'path';
+import { getSupportedExtensions } from '../utils/language-detection.js';
 
 export interface FileWatcherOptions {
   rootPath: string;
@@ -8,6 +10,19 @@ export interface FileWatcherOptions {
   onChanged: () => void;
 }
 
+const TRACKED_EXTENSIONS = new Set(
+  getSupportedExtensions().map((extension) => extension.toLowerCase())
+);
+
+const TRACKED_METADATA_FILES = new Set(['.gitignore']);
+
+function isTrackedSourcePath(filePath: string): boolean {
+  const basename = path.basename(filePath).toLowerCase();
+  if (TRACKED_METADATA_FILES.has(basename)) return true;
+  const extension = path.extname(filePath).toLowerCase();
+  return extension.length > 0 && TRACKED_EXTENSIONS.has(extension);
+}
+
 /**
  * Watch rootPath for source file changes and call onChanged (debounced).
  * Returns a stop() function that cancels the debounce timer and closes the watcher.
@@ -16,7 +31,8 @@ export function startFileWatcher(opts: FileWatcherOptions): () => void {
   const { rootPath, debounceMs = 2000, onChanged } = opts;
   let debounceTimer: ReturnType<typeof setTimeout> | undefined;
 
-  const trigger = () => {
+  const trigger = (filePath: string) => {
+    if (!isTrackedSourcePath(filePath)) return;
     if (debounceTimer !== undefined) clearTimeout(debounceTimer);
     debounceTimer = setTimeout(() => {
       debounceTimer = undefined;
diff --git a/tests/auto-refresh-e2e.test.ts b/tests/auto-refresh-e2e.test.ts
new file mode 100644
index 0000000..a7e0509
--- /dev/null
+++ b/tests/auto-refresh-e2e.test.ts
@@ -0,0 +1,145 @@
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { promises as fs } from 'fs';
+import os from 'os';
+import path from 'path';
+import { startFileWatcher } from '../src/core/file-watcher.js';
+import { createAutoRefreshController } from '../src/core/auto-refresh.js';
+import { CodebaseIndexer } from '../src/core/indexer.js';
+import {
+  CODEBASE_CONTEXT_DIRNAME,
+  KEYWORD_INDEX_FILENAME
+} from '../src/constants/codebase-context.js';
+
+type IndexStatus = 'idle' | 'indexing' | 'ready' | 'error';
+
+function sleep(ms: number): Promise<void> {
+  return new Promise((resolve) => setTimeout(resolve, ms));
+}
+
+function isRecord(value: unknown): value is Record<string, unknown> {
+  return typeof value === 'object' && value !== null;
+}
+
+function getKeywordChunks(raw: unknown): Array<Record<string, unknown>> {
+  if (Array.isArray(raw)) {
+    return raw.filter(isRecord);
+  }
+  if (!isRecord(raw)) return [];
+  if (!Array.isArray(raw.chunks)) return [];
+  return raw.chunks.filter(isRecord);
+}
+
+async function readIndexedContent(rootPath: string): Promise<string> {
+  const indexPath = path.join(rootPath, CODEBASE_CONTEXT_DIRNAME, KEYWORD_INDEX_FILENAME);
+  const raw = JSON.parse(await fs.readFile(indexPath, 'utf-8')) as unknown;
+  const chunks = getKeywordChunks(raw);
+  return chunks
+    .map((chunk) => (typeof chunk.content === 'string' ? chunk.content : ''))
+    .join('\n');
+}
+
+async function waitFor(
+  condition: () => Promise<boolean>,
+  timeoutMs: number,
+  intervalMs: number
+): Promise<void> {
+  const startedAt = Date.now();
+  let lastError: unknown;
+  while (Date.now() - startedAt < timeoutMs) {
+    try {
+      if (await condition()) return;
+      lastError = undefined;
+    } catch (error) {
+      lastError = error;
+    }
+    await sleep(intervalMs);
+  }
+  const reason =
+    lastError instanceof Error && lastError.message
+      ? ` Last transient error: ${lastError.message}`
+      : '';
+  throw new Error(`Timed out after ${timeoutMs}ms waiting for condition.${reason}`);
+}
+
+describe('Auto-refresh E2E', () => {
+  let tempDir: string;
+
+  beforeEach(async () => {
+    tempDir = await fs.mkdtemp(path.join(os.tmpdir(), 'auto-refresh-e2e-'));
+    await fs.mkdir(path.join(tempDir, 'src'), { recursive: true });
+    await fs.writeFile(path.join(tempDir, 'package.json'), JSON.stringify({ name: 'watch-test' }));
+    await fs.writeFile(path.join(tempDir, 'src', 'app.ts'), 'export const token = "INITIAL_TOKEN";\n');
+  });
+
+  afterEach(async () => {
+    await fs.rm(tempDir, { recursive: true, force: true });
+  });
+
+  it('updates index after a file edit without manual refresh_index', async () => {
+    await new CodebaseIndexer({
+      rootPath: tempDir,
+      config: { skipEmbedding: true }
+    }).index();
+
+    const initialContent = await readIndexedContent(tempDir);
+    expect(initialContent).toContain('INITIAL_TOKEN');
+    expect(initialContent).not.toContain('UPDATED_TOKEN');
+
+    const autoRefresh = createAutoRefreshController();
+    let indexStatus: IndexStatus = 'ready';
+    let incrementalRuns = 0;
+
+    const runIncrementalIndex = async (): Promise<void> => {
+      if (indexStatus === 'indexing') return;
+      indexStatus = 'indexing';
+
+      try {
+        await new CodebaseIndexer({
+          rootPath: tempDir,
+          config: { skipEmbedding: true },
+          incrementalOnly: true
+        }).index();
+        indexStatus = 'ready';
+      } catch (error) {
+        indexStatus = 'error';
+        throw error;
+      }
+
+      if (autoRefresh.consumeQueuedRefresh(indexStatus)) {
+        incrementalRuns++;
+        void runIncrementalIndex();
+      }
+    };
+
+    const stopWatcher = startFileWatcher({
+      rootPath: tempDir,
+      debounceMs: 200,
+      onChanged: () => {
+        const shouldRunNow = autoRefresh.onFileChange(indexStatus === 'indexing');
+        if (!shouldRunNow) return;
+        incrementalRuns++;
+        void runIncrementalIndex();
+      }
+    });
+
+    try {
+      await sleep(250);
+      await fs.writeFile(path.join(tempDir, 'src', 'app.ts'), 'export const token = "UPDATED_TOKEN";\n');
+
+      await waitFor(
+        async () => {
+          const content = await readIndexedContent(tempDir);
+          return content.includes('UPDATED_TOKEN');
+        },
+        15000,
+        200
+      );
+
+      const updatedContent = await readIndexedContent(tempDir);
+      expect(updatedContent).toContain('UPDATED_TOKEN');
+      expect(incrementalRuns).toBeGreaterThan(0);
+    } finally {
+      stopWatcher();
+    }
+  }, 20000);
+});
diff --git a/tests/file-watcher.test.ts b/tests/file-watcher.test.ts
index a1a6bc3..be36ba3 100644
--- a/tests/file-watcher.test.ts
+++ b/tests/file-watcher.test.ts
@@ -85,4 +85,48 @@ describe('FileWatcher', () => {
     await new Promise((resolve) => setTimeout(resolve, debounceMs + 200));
     expect(callCount).toBe(0);
   }, 5000);
+
+  it('ignores changes to non-tracked file extensions', async () => {
+    const debounceMs = 250;
+    let callCount = 0;
+
+    const stop = startFileWatcher({
+      rootPath: tempDir,
+      debounceMs,
+      onChanged: () => {
+        callCount++;
+      }
+    });
+
+    try {
+      await new Promise((resolve) => setTimeout(resolve, 100));
+      await fs.writeFile(path.join(tempDir, 'notes.txt'), 'this should be ignored');
+      await new Promise((resolve) => setTimeout(resolve, debounceMs + 700));
+      expect(callCount).toBe(0);
+    } finally {
+      stop();
+    }
+  }, 5000);
+
+  it('triggers on .gitignore changes', async () => {
+    const debounceMs = 250;
+    let callCount = 0;
+
+    const stop = startFileWatcher({
+      rootPath: tempDir,
+      debounceMs,
+      onChanged: () => {
+        callCount++;
+      }
+    });
+
+    try {
+      await new Promise((resolve) => setTimeout(resolve, 100));
+      await fs.writeFile(path.join(tempDir, '.gitignore'), 'dist/\n');
+      await new Promise((resolve) => setTimeout(resolve, debounceMs + 700));
+      expect(callCount).toBe(1);
+    } finally {
+      stop();
+    }
+  }, 5000);
 });