diff --git a/src/core/file-watcher.ts b/src/core/file-watcher.ts
index 4687466..58efb81 100644
--- a/src/core/file-watcher.ts
+++ b/src/core/file-watcher.ts
@@ -6,6 +6,8 @@ export interface FileWatcherOptions {
   rootPath: string;
   /** ms after last change before triggering. Default: 2000 */
   debounceMs?: number;
+  /** Called once chokidar finishes initial scan and starts emitting change events */
+  onReady?: () => void;
   /** Called once the debounce window expires after the last detected change */
   onChanged: () => void;
 }
@@ -28,7 +30,7 @@ function isTrackedSourcePath(filePath: string): boolean {
  * Returns a stop() function that cancels the debounce timer and closes the watcher.
  */
 export function startFileWatcher(opts: FileWatcherOptions): () => void {
-  const { rootPath, debounceMs = 2000, onChanged } = opts;
+  const { rootPath, debounceMs = 2000, onReady, onChanged } = opts;
   let debounceTimer: ReturnType<typeof setTimeout> | undefined;
 
   const trigger = (filePath: string) => {
@@ -59,6 +61,7 @@ export function startFileWatcher(opts: FileWatcherOptions): () => void {
   });
 
   watcher
+    .on('ready', () => onReady?.())
     .on('add', trigger)
     .on('change', trigger)
     .on('unlink', trigger)
diff --git a/tests/auto-refresh-e2e.test.ts b/tests/auto-refresh-e2e.test.ts
index a7e0509..6e6a7bc 100644
--- a/tests/auto-refresh-e2e.test.ts
+++ b/tests/auto-refresh-e2e.test.ts
@@ -5,6 +5,7 @@ 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 { rmWithRetries } from './test-helpers.js';
 import {
   CODEBASE_CONTEXT_DIRNAME,
   KEYWORD_INDEX_FILENAME
@@ -72,7 +73,7 @@ describe('Auto-refresh E2E', () => {
   });
 
   afterEach(async () => {
-    await fs.rm(tempDir, { recursive: true, force: true });
+    await rmWithRetries(tempDir);
   });
 
   it('updates index after a file edit without manual refresh_index', async () => {
@@ -111,9 +112,15 @@ describe('Auto-refresh E2E', () => {
       }
     };
 
+    let resolveReady!: () => void;
+    const watcherReady = new Promise<void>((resolve) => {
+      resolveReady = resolve;
+    });
+
     const stopWatcher = startFileWatcher({
       rootPath: tempDir,
       debounceMs: 200,
+      onReady: () => resolveReady(),
       onChanged: () => {
         const shouldRunNow = autoRefresh.onFileChange(indexStatus === 'indexing');
         if (!shouldRunNow) return;
@@ -123,7 +130,7 @@ describe('Auto-refresh E2E', () => {
     });
 
     try {
-      await sleep(250);
+      await watcherReady;
       await fs.writeFile(path.join(tempDir, 'src', 'app.ts'), 'export const token = "UPDATED_TOKEN";\n');
 
       await waitFor(
diff --git a/tests/file-watcher.test.ts b/tests/file-watcher.test.ts
index be36ba3..be3e38e 100644
--- a/tests/file-watcher.test.ts
+++ b/tests/file-watcher.test.ts
@@ -3,6 +3,7 @@ import { promises as fs } from 'fs';
 import path from 'path';
 import os from 'os';
 import { startFileWatcher } from '../src/core/file-watcher.js';
+import { rmWithRetries } from './test-helpers.js';
 
 describe('FileWatcher', () => {
   let tempDir: string;
@@ -12,22 +13,27 @@ describe('FileWatcher', () => {
   });
 
   afterEach(async () => {
-    await fs.rm(tempDir, { recursive: true, force: true });
+    await rmWithRetries(tempDir);
   });
 
   it('triggers onChanged after debounce window', async () => {
     const debounceMs = 400;
     let callCount = 0;
 
+    let resolveReady!: () => void;
+    const ready = new Promise<void>((resolve) => {
+      resolveReady = resolve;
+    });
+
     const stop = startFileWatcher({
       rootPath: tempDir,
       debounceMs,
+      onReady: () => resolveReady(),
       onChanged: () => { callCount++; },
     });
 
     try {
-      // Give chokidar a moment to finish initializing before the first write
-      await new Promise((resolve) => setTimeout(resolve, 100));
+      await ready;
       await fs.writeFile(path.join(tempDir, 'test.ts'), 'export const x = 1;');
       // Wait for chokidar to pick up the event (including awaitWriteFinish stabilityThreshold)
       // + debounce window + OS scheduling slack
@@ -39,25 +45,31 @@ describe('FileWatcher', () => {
   }, 8000);
 
   it('debounces rapid changes into a single callback', async () => {
-    const debounceMs = 300;
+    const debounceMs = 800;
     let callCount = 0;
 
+    let resolveReady!: () => void;
+    const ready = new Promise<void>((resolve) => {
+      resolveReady = resolve;
+    });
+
     const stop = startFileWatcher({
       rootPath: tempDir,
       debounceMs,
+      onReady: () => resolveReady(),
       onChanged: () => { callCount++; },
     });
 
     try {
       // Give chokidar a moment to finish initializing before the first write
-      await new Promise((resolve) => setTimeout(resolve, 100));
+      await ready;
       // Write 5 files in quick succession — all within the debounce window
       for (let i = 0; i < 5; i++) {
         await fs.writeFile(path.join(tempDir, `file${i}.ts`), `export const x${i} = ${i};`);
-        await new Promise((resolve) => setTimeout(resolve, 50));
+        await new Promise((resolve) => setTimeout(resolve, 20));
       }
       // Wait for debounce to settle
-      await new Promise((resolve) => setTimeout(resolve, debounceMs + 400));
+      await new Promise((resolve) => setTimeout(resolve, debounceMs + 1200));
       expect(callCount).toBe(1);
     } finally {
       stop();
@@ -68,14 +80,20 @@ describe('FileWatcher', () => {
     const debounceMs = 500;
     let callCount = 0;
 
+    let resolveReady!: () => void;
+    const ready = new Promise<void>((resolve) => {
+      resolveReady = resolve;
+    });
+
     const stop = startFileWatcher({
       rootPath: tempDir,
       debounceMs,
+      onReady: () => resolveReady(),
       onChanged: () => { callCount++; },
     });
 
     // Give chokidar a moment to finish initializing before the first write
-    await new Promise((resolve) => setTimeout(resolve, 100));
+    await ready;
     await fs.writeFile(path.join(tempDir, 'cancel.ts'), 'export const y = 99;');
     // Let chokidar detect the event (including awaitWriteFinish stabilityThreshold)
     // but stop before the debounce window expires.
@@ -90,16 +108,22 @@ describe('FileWatcher', () => {
     const debounceMs = 250;
     let callCount = 0;
 
+    let resolveReady!: () => void;
+    const ready = new Promise<void>((resolve) => {
+      resolveReady = resolve;
+    });
+
     const stop = startFileWatcher({
       rootPath: tempDir,
       debounceMs,
+      onReady: () => resolveReady(),
       onChanged: () => {
         callCount++;
       }
     });
 
     try {
-      await new Promise((resolve) => setTimeout(resolve, 100));
+      await ready;
       await fs.writeFile(path.join(tempDir, 'notes.txt'), 'this should be ignored');
       await new Promise((resolve) => setTimeout(resolve, debounceMs + 700));
       expect(callCount).toBe(0);
@@ -112,16 +136,22 @@ describe('FileWatcher', () => {
     const debounceMs = 250;
     let callCount = 0;
 
+    let resolveReady!: () => void;
+    const ready = new Promise<void>((resolve) => {
+      resolveReady = resolve;
+    });
+
     const stop = startFileWatcher({
       rootPath: tempDir,
       debounceMs,
+      onReady: () => resolveReady(),
       onChanged: () => {
         callCount++;
       }
     });
 
     try {
-      await new Promise((resolve) => setTimeout(resolve, 100));
+      await ready;
       await fs.writeFile(path.join(tempDir, '.gitignore'), 'dist/\n');
       await new Promise((resolve) => setTimeout(resolve, debounceMs + 700));
       expect(callCount).toBe(1);
diff --git a/tests/impact-2hop.test.ts b/tests/impact-2hop.test.ts
index 40e22d9..f284b64 100644
--- a/tests/impact-2hop.test.ts
+++ b/tests/impact-2hop.test.ts
@@ -1,9 +1,11 @@
 import { describe, it, expect, beforeEach, afterEach } from 'vitest';
 import { promises as fs } from 'fs';
+import os from 'os';
 import path from 'path';
 import { CodebaseIndexer } from '../src/core/indexer.js';
 import { dispatchTool } from '../src/tools/index.js';
 import type { ToolContext } from '../src/tools/types.js';
+import { rmWithRetries } from './test-helpers.js';
 import {
   CODEBASE_CONTEXT_DIRNAME,
   INTELLIGENCE_FILENAME,
@@ -18,8 +20,7 @@ describe('Impact candidates (2-hop)', () => {
   const token = 'UNIQUETOKEN123';
 
   beforeEach(async () => {
-    // Keep test artifacts under CWD (mirrors other indexer tests and avoids OS tmp quirks)
-    tempRoot = await fs.mkdtemp(path.join(process.cwd(), '.tmp-impact-2hop-'));
+    tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), 'impact-2hop-'));
     const srcDir = path.join(tempRoot, 'src');
     await fs.mkdir(srcDir, { recursive: true });
     await fs.writeFile(path.join(tempRoot, 'package.json'), JSON.stringify({ name: 'impact-2hop' }));
@@ -40,7 +41,7 @@ describe('Impact candidates (2-hop)', () => {
 
   afterEach(async () => {
     if (tempRoot) {
-      await fs.rm(tempRoot, { recursive: true, force: true });
+      await rmWithRetries(tempRoot);
       tempRoot = null;
     }
   });
diff --git a/tests/search-snippets.test.ts b/tests/search-snippets.test.ts
index afa8974..5f90ba0 100644
--- a/tests/search-snippets.test.ts
+++ b/tests/search-snippets.test.ts
@@ -3,6 +3,7 @@ import { promises as fs } from 'fs';
 import os from 'os';
 import path from 'path';
 import { CodebaseIndexer } from '../src/core/indexer.js';
+import { rmWithRetries } from './test-helpers.js';
 
 describe('Search Snippets with Scope Headers', () => {
   let tempRoot: string | null = null;
@@ -91,15 +92,15 @@ export const VERSION = '1.0.0';
       config: { skipEmbedding: true }
     });
     await indexer.index();
-  });
+  }, 30000);
 
   afterEach(async () => {
     if (tempRoot) {
-      await fs.rm(tempRoot, { recursive: true, force: true });
+      await rmWithRetries(tempRoot);
       tempRoot = null;
     }
     delete process.env.CODEBASE_ROOT;
-  });
+  }, 30000);
 
   it('returns snippets when includeSnippets=true', async () => {
     if (!tempRoot) throw new Error('tempRoot not initialized');
diff --git a/tests/test-helpers.ts b/tests/test-helpers.ts
new file mode 100644
index 0000000..4993a73
--- /dev/null
+++ b/tests/test-helpers.ts
@@ -0,0 +1,19 @@
+import { promises as fs } from 'fs';
+
+export async function rmWithRetries(targetPath: string): Promise<void> {
+  const maxAttempts = 8;
+  let delayMs = 25;
+
+  for (let attempt = 1; attempt <= maxAttempts; attempt++) {
+    try {
+      await fs.rm(targetPath, { recursive: true, force: true });
+      return;
+    } catch (error) {
+      const code = (error as { code?: string }).code;
+      const retryable = code === 'ENOTEMPTY' || code === 'EPERM' || code === 'EBUSY';
+      if (!retryable || attempt === maxAttempts) throw error;
+      await new Promise((resolve) => setTimeout(resolve, delayMs));
+      delayMs *= 2;
+    }
+  }
+}