chore: bump version to 10.3.2

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.claude-plugin/marketplace.json

@@ -10,7 +10,7 @@
   "plugins": [
     {
       "name": "claude-mem",
-      "version": "10.3.0",
+      "version": "10.3.2",
       "source": "./plugin",
       "description": "Persistent memory system for Claude Code - context compression across sessions"
     }

.gitignore

@@ -1,6 +1,7 @@
 datasets/
 node_modules/
 dist/
+!installer/dist/
 *.log
 .DS_Store
 .env

CHANGELOG.md

@@ -2,6 +2,46 @@
 
 All notable changes to claude-mem.
 
+## [v10.3.1] - 2026-02-19
+
+## Fix: Prevent Duplicate Worker Daemons and Zombie Processes
+
+Three root causes of chroma-mcp timeouts identified and fixed:
+
+### PID-based daemon guard
+Exit immediately on startup if PID file points to a live process. Prevents the race condition where hooks firing simultaneously could start multiple daemons before either wrote a PID file.
+
+### Port-based daemon guard
+Exit if port 37777 is already bound — runs before WorkerService constructor registers keepalive signal handlers that previously prevented exit on EADDRINUSE.
+
+### Guaranteed process.exit() after HTTP shutdown
+HTTP shutdown (POST /api/admin/shutdown) now calls `process.exit(0)` in a `try/finally` block. Previously, zombie workers stayed alive after shutdown, and background tasks reconnected to chroma-mcp, spawning duplicate subprocesses contending for the same data directory.
+
+## [v10.3.0] - 2026-02-18
+
+## Replace WASM Embeddings with Persistent chroma-mcp MCP Connection
+
+### Highlights
+
+- **New: ChromaMcpManager** — Singleton stdio MCP client communicating with chroma-mcp via `uvx`, replacing the previous ChromaServerManager (`npx chroma run` + `chromadb` npm + ONNX/WASM)
+- **Eliminates native binary issues** — No more segfaults, WASM embedding failures, or cross-platform install headaches
+- **Graceful subprocess lifecycle** — Wired into GracefulShutdown for clean teardown; zombie process prevention with kill-on-failure and stale `onclose` handler guards
+- **Connection backoff** — 10-second reconnect backoff prevents chroma-mcp spawn storms
+- **SQL injection guards** — Added parameterization to ChromaSync ID exclusion queries
+- **Simplified ChromaSync** — Reduced complexity by delegating embedding concerns to chroma-mcp
+
+### Breaking Changes
+
+None — backward compatible. ChromaDB data is preserved; only the connection mechanism changed.
+
+### Files Changed
+
+- `src/services/sync/ChromaMcpManager.ts` (new) — MCP client singleton
+- `src/services/sync/ChromaServerManager.ts` (deleted) — Old WASM/native approach
+- `src/services/sync/ChromaSync.ts` — Simplified to use MCP client
+- `src/services/worker-service.ts` — Updated startup sequence
+- `src/services/infrastructure/GracefulShutdown.ts` — Subprocess cleanup integration
+
 ## [v10.2.6] - 2026-02-18
 
 ## Bug Fixes
@@ -1411,32 +1451,3 @@ Thanks @yungweng for the detailed bug report!
 - Updated worker CLI scripts to reference worker-service.cjs directly
 - Simplified hook command configurations
 
-## [v8.2.8] - 2025-12-29
-
-## Bug Fixes
-
-- Fixed orphaned chroma-mcp processes during shutdown (#489)
-  - Added graceful shutdown handling with signal handlers registered early in WorkerService lifecycle
-  - Ensures ChromaSync subprocess cleanup even when interrupted during initialization
-  - Removes PID file during shutdown to prevent stale process tracking
-
-## Technical Details
-
-This patch release addresses a race condition where SIGTERM/SIGINT signals arriving during ChromaSync initialization could leave orphaned chroma-mcp processes. The fix moves signal handler registration from the start() method to the constructor, ensuring cleanup handlers exist throughout the entire initialization lifecycle.
-
-**Full Changelog**: https://github.com/thedotmack/claude-mem/compare/v8.2.7...v8.2.8
-
-## [v8.2.7] - 2025-12-29
-
-## What's Changed
-
-### Token Optimizations
-- Simplified MCP server tool definitions for reduced token usage
-- Removed outdated troubleshooting and mem-search skill documentation
-- Enhanced search parameter descriptions for better clarity
-- Streamlined MCP workflows for improved efficiency
-
-This release significantly reduces the token footprint of the plugin's MCP tools and documentation.
-
-**Full Changelog**: https://github.com/thedotmack/claude-mem/compare/v8.2.6...v8.2.7
-

README.md

@@ -198,7 +198,7 @@ See [Architecture Overview](https://docs.claude-mem.ai/architecture/overview) fo
 
 ## MCP Search Tools
 
-Claude-Mem provides intelligent memory search through **5 MCP tools** following a token-efficient **3-layer workflow pattern**:
+Claude-Mem provides intelligent memory search through **4 MCP tools** following a token-efficient **3-layer workflow pattern**:
 
 **The 3-Layer Workflow:**
 
@@ -211,7 +211,6 @@ Claude-Mem provides intelligent memory search through **5 MCP tools** following
 - Start with `search` to get an index of results
 - Use `timeline` to see what was happening around specific observations
 - Use `get_observations` to fetch full details for relevant IDs
-- Use `save_memory` to manually store important information
 - **~10x token savings** by filtering before fetching details
 
 **Available MCP Tools:**
@@ -219,8 +218,6 @@ Claude-Mem provides intelligent memory search through **5 MCP tools** following
 1. **`search`** - Search memory index with full-text queries, filters by type/date/project
 2. **`timeline`** - Get chronological context around a specific observation or query
 3. **`get_observations`** - Fetch full observation details by IDs (always batch multiple IDs)
-4. **`save_memory`** - Manually save a memory/observation for semantic search
-5. **`__IMPORTANT`** - Workflow documentation (always visible to Claude)
 
 **Example Usage:**
 
@@ -232,9 +229,6 @@ search(query="authentication bug", type="bugfix", limit=10)
 
 // Step 3: Fetch full details
 get_observations(ids=[123, 456])
-
-// Save important information manually
-save_memory(text="API requires auth header X-API-Key", title="API Auth")
 ```
 
 See [Search Tools Guide](https://docs.claude-mem.ai/usage/search-tools) for detailed examples.

install/public/install.sh

@@ -5,7 +5,7 @@ set -euo pipefail
 # Usage: curl -fsSL https://install.cmem.ai | bash
 #   or:  curl -fsSL https://install.cmem.ai | bash -s -- --provider=gemini --api-key=YOUR_KEY
 
-INSTALLER_URL="https://raw.githubusercontent.com/thedotmack/claude-mem/main/installer/dist/index.js"
+INSTALLER_URL="https://install.cmem.ai/installer.js"
 
 # Colors
 RED='\033[0;31m'

install/vercel.json

@@ -1,5 +1,8 @@
 {
   "$schema": "https://openapi.vercel.sh/vercel.json",
+  "rewrites": [
+    { "source": "/", "destination": "/install.sh" }
+  ],
   "headers": [
     {
       "source": "/(.*)\\.sh",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "claude-mem",
-  "version": "10.3.0",
+  "version": "10.3.2",
   "description": "Memory compression system for Claude Code - persist context across sessions",
   "keywords": [
     "claude",

plan.md

@@ -0,0 +1,52 @@
+# Fix: SessionStart Hook "startup hook error" — Worker Not Waiting
+
+## Root Cause
+
+The **installed plugin** (`~/.claude/plugins/marketplaces/thedotmack/`) is version **10.2.5** and has **none** of the recent fixes:
+
+| Fix | Repo Status | Installed Status |
+|-----|-------------|-----------------|
+| Hook group split (smart-install isolated from worker start) | In `plugin/hooks/hooks.json` | **Missing** — all 3 hooks in one group, smart-install failure blocks worker |
+| `waitForReadiness()` after spawn | In `src/services/infrastructure/HealthMonitor.ts` | **Missing** — 0 occurrences in installed `worker-service.cjs` |
+| Early `initializationCompleteFlag` (after DB+search, not MCP) | In `src/services/worker-service.ts` | **Missing** — flag set after MCP connection (5+ minute wait) |
+
+The changes exist in source code but were **never built and synced** to the installed location.
+
+---
+
+## Phase 1: Build and Sync
+
+```bash
+npm run build-and-sync
+```
+
+### Verification
+
+```bash
+# 1. Confirm waitForReadiness exists in installed build
+grep -c "waitForReadiness" ~/.claude/plugins/marketplaces/thedotmack/plugin/scripts/worker-service.cjs
+# Expected: > 0
+
+# 2. Confirm hooks.json has two SessionStart groups (the split)
+python3 -c "import json; d=json.load(open('$(echo $HOME)/.claude/plugins/marketplaces/thedotmack/plugin/hooks/hooks.json')); print('SessionStart groups:', len(d['hooks']['SessionStart']))"
+# Expected: 2
+
+# 3. Confirm initializationCompleteFlag is set before MCP connection
+grep -n "Core initialization complete" ~/.claude/plugins/marketplaces/thedotmack/plugin/scripts/worker-service.cjs | head -1
+# Expected: appears BEFORE "MCP server connected"
+```
+
+## Phase 2: Restart Worker and Test
+
+```bash
+# Stop existing worker
+bun plugin/scripts/worker-service.cjs stop
+
+# Verify stopped
+curl -s http://127.0.0.1:37777/api/health && echo "STILL RUNNING" || echo "STOPPED"
+```
+
+Then start a new Claude Code session and verify:
+- No "SessionStart:startup hook error" messages
+- Worker is running: `curl http://127.0.0.1:37777/api/health`
+- Readiness endpoint works: `curl http://127.0.0.1:37777/api/readiness`

plugin/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "claude-mem",
-  "version": "10.3.0",
+  "version": "10.3.2",
   "description": "Persistent memory system for Claude Code - seamlessly preserve context across sessions",
   "author": {
     "name": "Alex Newman"

plugin/hooks/hooks.json

@@ -21,7 +21,12 @@
             "type": "command",
             "command": "node \"${CLAUDE_PLUGIN_ROOT}/scripts/smart-install.js\"",
             "timeout": 300
-          },
+          }
+        ]
+      },
+      {
+        "matcher": "startup|clear|compact",
+        "hooks": [
           {
             "type": "command",
             "command": "node \"${CLAUDE_PLUGIN_ROOT}/scripts/bun-runner.js\" \"${CLAUDE_PLUGIN_ROOT}/scripts/worker-service.cjs\" start",

plugin/package.json

@@ -1,6 +1,6 @@
 {
   "name": "claude-mem-plugin",
-  "version": "10.3.0",
+  "version": "10.3.2",
   "private": true,
   "description": "Runtime dependencies for claude-mem bundled hooks",
   "type": "module",

plugin/skills/mem-search/SKILL.md

@@ -93,20 +93,6 @@ get_observations(ids=[11131, 10942])
 
 **Returns:** Complete observation objects with title, subtitle, narrative, facts, concepts, files (~500-1000 tokens each)
 
-## Saving Memories
-
-Use the `save_memory` MCP tool to store manual observations:
-
-```
-save_memory(text="Important discovery about the auth system", title="Auth Architecture", project="my-project")
-```
-
-**Parameters:**
-
-- `text` (string, required) - Content to remember
-- `title` (string, optional) - Short title, auto-generated if omitted
-- `project` (string, optional) - Project name, defaults to "claude-mem"
-
 ## Examples
 
 **Find recent bug fixes:**

src/servers/mcp-server.ts

@@ -235,8 +235,8 @@ NEVER fetch full details without filtering first. 10x token savings.`,
     }
   },
   {
-    name: 'save_memory',
-    description: 'Save a manual memory/observation for semantic search. Use this to remember important information.',
+    name: 'save_observation',
+    description: 'Save an observation to the database. Params: text (required), title, project',
     inputSchema: {
       type: 'object',
       properties: {

src/services/context/formatters/ColorFormatter.ts

@@ -74,8 +74,8 @@ export function renderColorContextIndex(): string[] {
     `${colors.dim}Context Index: This semantic index (titles, types, files, tokens) is usually sufficient to understand past work.${colors.reset}`,
     '',
     `${colors.dim}When you need implementation details, rationale, or debugging context:${colors.reset}`,
-    `${colors.dim}  - Use MCP tools (search, get_observations) to fetch full observations on-demand${colors.reset}`,
-    `${colors.dim}  - Critical types ( bugfix, decision) often need detailed fetching${colors.reset}`,
+    `${colors.dim}  - Fetch by ID: get_observations([IDs]) for observations visible in this index${colors.reset}`,
+    `${colors.dim}  - Search history: Use the mem-search skill for past decisions, bugs, and deeper research${colors.reset}`,
     `${colors.dim}  - Trust this index over re-reading code for past decisions and learnings${colors.reset}`,
     ''
   ];

src/services/context/formatters/MarkdownFormatter.ts

@@ -72,8 +72,8 @@ export function renderMarkdownContextIndex(): string[] {
     `**Context Index:** This semantic index (titles, types, files, tokens) is usually sufficient to understand past work.`,
     '',
     `When you need implementation details, rationale, or debugging context:`,
-    `- Use MCP tools (search, get_observations) to fetch full observations on-demand`,
-    `- Critical types ( bugfix, decision) often need detailed fetching`,
+    `- Fetch by ID: get_observations([IDs]) for observations visible in this index`,
+    `- Search history: Use the mem-search skill for past decisions, bugs, and deeper research`,
     `- Trust this index over re-reading code for past decisions and learnings`,
     ''
   ];

src/services/infrastructure/HealthMonitor.ts

@@ -29,31 +29,49 @@ export async function isPortInUse(port: number): Promise<boolean> {
 }
 
 /**
- * Wait for the worker HTTP server to become responsive (liveness check)
- * Uses /api/health instead of /api/readiness because:
- * - /api/health returns 200 as soon as HTTP server is listening
- * - /api/readiness waits for full initialization (MCP connection can take 5+ minutes)
- * See: https://github.com/thedotmack/claude-mem/issues/811
- * @param port Worker port to check
- * @param timeoutMs Maximum time to wait in milliseconds
- * @returns true if worker became responsive, false if timeout
+ * Poll a localhost endpoint until it returns 200 OK or timeout.
+ * Shared implementation for liveness and readiness checks.
  */
-export async function waitForHealth(port: number, timeoutMs: number = 30000): Promise<boolean> {
+async function pollEndpointUntilOk(
+  port: number,
+  endpointPath: string,
+  timeoutMs: number,
+  retryLogMessage: string
+): Promise<boolean> {
   const start = Date.now();
   while (Date.now() - start < timeoutMs) {
     try {
       // Note: Removed AbortSignal.timeout to avoid Windows Bun cleanup issue (libuv assertion)
-      const response = await fetch(`http://127.0.0.1:${port}/api/health`);
+      const response = await fetch(`http://127.0.0.1:${port}${endpointPath}`);
       if (response.ok) return true;
     } catch (error) {
       // [ANTI-PATTERN IGNORED]: Retry loop - expected failures during startup, will retry
-      logger.debug('SYSTEM', 'Service not ready yet, will retry', { port }, error as Error);
+      logger.debug('SYSTEM', retryLogMessage, { port }, error as Error);
     }
     await new Promise(r => setTimeout(r, 500));
   }
   return false;
 }
 
+/**
+ * Wait for the worker HTTP server to become responsive (liveness check).
+ * Uses /api/health which returns 200 as soon as the HTTP server is listening.
+ * For full initialization (DB + search), use waitForReadiness() instead.
+ */
+export function waitForHealth(port: number, timeoutMs: number = 30000): Promise<boolean> {
+  return pollEndpointUntilOk(port, '/api/health', timeoutMs, 'Service not ready yet, will retry');
+}
+
+/**
+ * Wait for the worker to be fully initialized (DB + search ready).
+ * Uses /api/readiness which returns 200 only after core initialization completes.
+ * Now that initializationCompleteFlag is set after DB/search init (not MCP),
+ * this typically completes in a few seconds.
+ */
+export function waitForReadiness(port: number, timeoutMs: number = 30000): Promise<boolean> {
+  return pollEndpointUntilOk(port, '/api/readiness', timeoutMs, 'Worker not ready yet, will retry');
+}
+
 /**
  * Wait for a port to become free (no longer responding to health checks)
  * Used after shutdown to confirm the port is available for restart

src/services/infrastructure/ProcessManager.ts

@@ -10,7 +10,7 @@
 
 import path from 'path';
 import { homedir } from 'os';
-import { existsSync, writeFileSync, readFileSync, unlinkSync, mkdirSync } from 'fs';
+import { existsSync, writeFileSync, readFileSync, unlinkSync, mkdirSync, rmSync } from 'fs';
 import { exec, execSync, spawn } from 'child_process';
 import { promisify } from 'util';
 import { logger } from '../../utils/logger.js';
@@ -426,6 +426,182 @@ export async function cleanupOrphanedProcesses(): Promise<void> {
   logger.info('SYSTEM', 'Orphaned processes cleaned up', { count: pidsToKill.length });
 }
 
+// Patterns that should be killed immediately at startup (no age gate)
+// These are child processes that should not outlive their parent worker
+const AGGRESSIVE_CLEANUP_PATTERNS = ['worker-service.cjs', 'chroma-mcp'];
+
+// Patterns that keep the age-gated threshold (may be legitimately running)
+const AGE_GATED_CLEANUP_PATTERNS = ['mcp-server.cjs'];
+
+/**
+ * Aggressive startup cleanup for orphaned claude-mem processes.
+ *
+ * Unlike cleanupOrphanedProcesses() which age-gates everything at 30 minutes,
+ * this function kills worker-service.cjs and chroma-mcp processes immediately
+ * (they should not outlive their parent worker). Only mcp-server.cjs keeps
+ * the age threshold since it may be legitimately running.
+ *
+ * Called once at daemon startup.
+ */
+export async function aggressiveStartupCleanup(): Promise<void> {
+  const isWindows = process.platform === 'win32';
+  const currentPid = process.pid;
+  const pidsToKill: number[] = [];
+  const allPatterns = [...AGGRESSIVE_CLEANUP_PATTERNS, ...AGE_GATED_CLEANUP_PATTERNS];
+
+  try {
+    if (isWindows) {
+      const patternConditions = allPatterns
+        .map(p => `$_.CommandLine -like '*${p}*'`)
+        .join(' -or ');
+
+      const cmd = `powershell -NoProfile -NonInteractive -Command "Get-CimInstance Win32_Process | Where-Object { (${patternConditions}) -and $_.ProcessId -ne ${currentPid} } | Select-Object ProcessId, CommandLine, CreationDate | ConvertTo-Json"`;
+      const { stdout } = await execAsync(cmd, { timeout: HOOK_TIMEOUTS.POWERSHELL_COMMAND });
+
+      if (!stdout.trim() || stdout.trim() === 'null') {
+        logger.debug('SYSTEM', 'No orphaned claude-mem processes found (Windows)');
+        return;
+      }
+
+      const processes = JSON.parse(stdout);
+      const processList = Array.isArray(processes) ? processes : [processes];
+      const now = Date.now();
+
+      for (const proc of processList) {
+        const pid = proc.ProcessId;
+        if (!Number.isInteger(pid) || pid <= 0 || pid === currentPid) continue;
+
+        const commandLine = proc.CommandLine || '';
+        const isAggressive = AGGRESSIVE_CLEANUP_PATTERNS.some(p => commandLine.includes(p));
+
+        if (isAggressive) {
+          // Kill immediately — no age check
+          pidsToKill.push(pid);
+          logger.debug('SYSTEM', 'Found orphaned process (aggressive)', { pid, commandLine: commandLine.substring(0, 80) });
+        } else {
+          // Age-gated: only kill if older than threshold
+          const creationMatch = proc.CreationDate?.match(/\/Date\((\d+)\)\//);
+          if (creationMatch) {
+            const creationTime = parseInt(creationMatch[1], 10);
+            const ageMinutes = (now - creationTime) / (1000 * 60);
+            if (ageMinutes >= ORPHAN_MAX_AGE_MINUTES) {
+              pidsToKill.push(pid);
+              logger.debug('SYSTEM', 'Found orphaned process (age-gated)', { pid, ageMinutes: Math.round(ageMinutes) });
+            }
+          }
+        }
+      }
+    } else {
+      // Unix: Use ps with elapsed time
+      const patternRegex = allPatterns.join('|');
+      const { stdout } = await execAsync(
+        `ps -eo pid,etime,command | grep -E "${patternRegex}" | grep -v grep || true`
+      );
+
+      if (!stdout.trim()) {
+        logger.debug('SYSTEM', 'No orphaned claude-mem processes found (Unix)');
+        return;
+      }
+
+      const lines = stdout.trim().split('\n');
+      for (const line of lines) {
+        const match = line.trim().match(/^(\d+)\s+(\S+)\s+(.*)$/);
+        if (!match) continue;
+
+        const pid = parseInt(match[1], 10);
+        const etime = match[2];
+        const command = match[3];
+
+        if (!Number.isInteger(pid) || pid <= 0 || pid === currentPid) continue;
+
+        const isAggressive = AGGRESSIVE_CLEANUP_PATTERNS.some(p => command.includes(p));
+
+        if (isAggressive) {
+          // Kill immediately — no age check
+          pidsToKill.push(pid);
+          logger.debug('SYSTEM', 'Found orphaned process (aggressive)', { pid, command: command.substring(0, 80) });
+        } else {
+          // Age-gated: only kill if older than threshold
+          const ageMinutes = parseElapsedTime(etime);
+          if (ageMinutes >= ORPHAN_MAX_AGE_MINUTES) {
+            pidsToKill.push(pid);
+            logger.debug('SYSTEM', 'Found orphaned process (age-gated)', { pid, ageMinutes, command: command.substring(0, 80) });
+          }
+        }
+      }
+    }
+  } catch (error) {
+    logger.error('SYSTEM', 'Failed to enumerate orphaned processes during aggressive cleanup', {}, error as Error);
+    return;
+  }
+
+  if (pidsToKill.length === 0) {
+    return;
+  }
+
+  logger.info('SYSTEM', 'Aggressive startup cleanup: killing orphaned processes', {
+    platform: isWindows ? 'Windows' : 'Unix',
+    count: pidsToKill.length,
+    pids: pidsToKill
+  });
+
+  if (isWindows) {
+    for (const pid of pidsToKill) {
+      if (!Number.isInteger(pid) || pid <= 0) continue;
+      try {
+        execSync(`taskkill /PID ${pid} /T /F`, { timeout: HOOK_TIMEOUTS.POWERSHELL_COMMAND, stdio: 'ignore' });
+      } catch (error) {
+        logger.debug('SYSTEM', 'Failed to kill process, may have already exited', { pid }, error as Error);
+      }
+    }
+  } else {
+    for (const pid of pidsToKill) {
+      try {
+        process.kill(pid, 'SIGKILL');
+      } catch (error) {
+        logger.debug('SYSTEM', 'Process already exited', { pid }, error as Error);
+      }
+    }
+  }
+
+  logger.info('SYSTEM', 'Aggressive startup cleanup complete', { count: pidsToKill.length });
+}
+
+const CHROMA_MIGRATION_MARKER_FILENAME = '.chroma-cleaned-v10.3';
+
+/**
+ * One-time chroma data wipe for users upgrading from versions with duplicate
+ * worker bugs that could corrupt chroma data. Since chroma is always rebuildable
+ * from SQLite (via backfillAllProjects), this is safe.
+ *
+ * Checks for a marker file. If absent, wipes ~/.claude-mem/chroma/ and writes
+ * the marker. If present, skips. Idempotent.
+ *
+ * @param dataDirectory - Override for DATA_DIR (used in tests)
+ */
+export function runOneTimeChromaMigration(dataDirectory?: string): void {
+  const effectiveDataDir = dataDirectory ?? DATA_DIR;
+  const markerPath = path.join(effectiveDataDir, CHROMA_MIGRATION_MARKER_FILENAME);
+  const chromaDir = path.join(effectiveDataDir, 'chroma');
+
+  if (existsSync(markerPath)) {
+    logger.debug('SYSTEM', 'Chroma migration marker exists, skipping wipe');
+    return;
+  }
+
+  logger.warn('SYSTEM', 'Running one-time chroma data wipe (upgrade from pre-v10.3)', { chromaDir });
+
+  if (existsSync(chromaDir)) {
+    rmSync(chromaDir, { recursive: true, force: true });
+    logger.info('SYSTEM', 'Chroma data directory removed', { chromaDir });
+  }
+
+  // Write marker file to prevent future wipes
+  mkdirSync(effectiveDataDir, { recursive: true });
+  writeFileSync(markerPath, new Date().toISOString());
+  logger.info('SYSTEM', 'Chroma migration marker written', { markerPath });
+}
+
 /**
  * Spawn a detached daemon process
  * Returns the child PID or undefined if spawn failed

src/services/server/Server.ts

@@ -248,8 +248,14 @@ export class Server {
         process.send!({ type: 'restart' });
       } else {
         // Unix or standalone Windows - handle restart ourselves
+        // The spawner (ensureWorkerStarted/restart command) handles spawning the new daemon.
+        // This process just needs to shut down and exit.
         setTimeout(async () => {
-          await this.options.onRestart();
+          try {
+            await this.options.onRestart();
+          } finally {
+            process.exit(0);
+          }
         }, 100);
       }
     });
@@ -268,7 +274,14 @@ export class Server {
       } else {
         // Unix or standalone Windows - handle shutdown ourselves
         setTimeout(async () => {
-          await this.options.onShutdown();
+          try {
+            await this.options.onShutdown();
+          } finally {
+            // CRITICAL: Exit the process after shutdown completes (or fails).
+            // Without this, the daemon stays alive as a zombie — background tasks
+            // (backfill, reconnects) keep running and respawn chroma-mcp subprocesses.
+            process.exit(0);
+          }
         }, 100);
       }
     });

src/services/worker-service.ts

@@ -69,14 +69,17 @@ import {
   readPidFile,
   removePidFile,
   getPlatformTimeout,
-  cleanupOrphanedProcesses,
+  aggressiveStartupCleanup,
+  runOneTimeChromaMigration,
   cleanStalePidFile,
+  isProcessAlive,
   spawnDaemon,
   createSignalHandler
 } from './infrastructure/ProcessManager.js';
 import {
   isPortInUse,
   waitForHealth,
+  waitForReadiness,
   waitForPortFree,
   httpShutdown,
   checkVersionMatch
@@ -367,7 +370,7 @@ export class WorkerService {
    */
   private async initializeBackground(): Promise<void> {
     try {
-      await cleanupOrphanedProcesses();
+      await aggressiveStartupCleanup();
 
       // Load mode configuration
       const { ModeManager } = await import('./domain/ModeManager.js');
@@ -376,6 +379,12 @@ export class WorkerService {
 
       const settings = SettingsDefaultsManager.loadFromFile(USER_SETTINGS_PATH);
 
+      // One-time chroma wipe for users upgrading from versions with duplicate worker bugs.
+      // Only runs in local mode (chroma is local-only). Backfill at line ~414 rebuilds from SQLite.
+      if (settings.CLAUDE_MEM_MODE === 'local' || !settings.CLAUDE_MEM_MODE) {
+        runOneTimeChromaMigration();
+      }
+
       // Initialize ChromaMcpManager (lazy - connects on first use via ChromaSync)
       this.chromaMcpManager = ChromaMcpManager.getInstance();
       logger.info('SYSTEM', 'ChromaMcpManager initialized (lazy - connects on first use)');
@@ -408,6 +417,13 @@ export class WorkerService {
       this.server.registerRoutes(this.searchRoutes);
       logger.info('WORKER', 'SearchManager initialized and search routes registered');
 
+      // DB and search are ready — mark initialization complete so hooks can proceed.
+      // MCP connection is tracked separately via mcpReady and is NOT required for
+      // the worker to serve context/search requests.
+      this.initializationCompleteFlag = true;
+      this.resolveInitialization();
+      logger.info('SYSTEM', 'Core initialization complete (DB + search ready)');
+
       // Auto-backfill Chroma for all projects if out of sync with SQLite (fire-and-forget)
       if (this.chromaMcpManager) {
         ChromaSync.backfillAllProjects().then(() => {
@@ -433,11 +449,7 @@ export class WorkerService {
 
       await Promise.race([mcpConnectionPromise, timeoutPromise]);
       this.mcpReady = true;
-      logger.success('WORKER', 'Connected to MCP server');
-
-      this.initializationCompleteFlag = true;
-      this.resolveInitialization();
-      logger.info('SYSTEM', 'Background initialization complete');
+      logger.success('WORKER', 'MCP server connected');
 
       // Start orphan reaper to clean up zombie processes (Issue #737)
       this.stopOrphanReaper = startOrphanReaper(() => {
@@ -937,6 +949,13 @@ async function ensureWorkerStarted(port: number): Promise<boolean> {
     return false;
   }
 
+  // Health passed (HTTP listening). Now wait for DB + search initialization
+  // so hooks that run immediately after can actually use the worker.
+  const ready = await waitForReadiness(port, getPlatformTimeout(HOOK_TIMEOUTS.READINESS_WAIT));
+  if (!ready) {
+    logger.warn('SYSTEM', 'Worker is alive but readiness timed out — proceeding anyway');
+  }
+
   clearWorkerSpawnAttempted();
   logger.info('SYSTEM', 'Worker started successfully');
   return true;
@@ -1097,6 +1116,28 @@ async function main() {
 
     case '--daemon':
     default: {
+      // GUARD 1: Refuse to start if another worker is already alive (PID check).
+      // Instant check (kill -0) — no HTTP dependency.
+      const existingPidInfo = readPidFile();
+      if (existingPidInfo && isProcessAlive(existingPidInfo.pid)) {
+        logger.info('SYSTEM', 'Worker already running (PID alive), refusing to start duplicate', {
+          existingPid: existingPidInfo.pid,
+          existingPort: existingPidInfo.port,
+          startedAt: existingPidInfo.startedAt
+        });
+        process.exit(0);
+      }
+
+      // GUARD 2: Refuse to start if the port is already bound.
+      // Catches the race where two daemons start simultaneously before
+      // either writes a PID file. Must run BEFORE constructing WorkerService
+      // because the constructor registers signal handlers and timers that
+      // prevent the process from exiting even if listen() fails later.
+      if (await isPortInUse(port)) {
+        logger.info('SYSTEM', 'Port already in use, refusing to start duplicate', { port });
+        process.exit(0);
+      }
+
       // Prevent daemon from dying silently on unhandled errors.
       // The HTTP server can continue serving even if a background task throws.
       process.on('unhandledRejection', (reason) => {

src/shared/hook-constants.ts

@@ -2,6 +2,7 @@ export const HOOK_TIMEOUTS = {
   DEFAULT: 300000,            // Standard HTTP timeout (5 min for slow systems)
   HEALTH_CHECK: 3000,         // Worker health check (3s — healthy worker responds in <100ms)
   POST_SPAWN_WAIT: 5000,      // Wait for daemon to start after spawn (starts in <1s on Linux)
+  READINESS_WAIT: 30000,      // Wait for DB + search init after spawn (typically <5s)
   PORT_IN_USE_WAIT: 3000,     // Wait when port occupied but health failing
   WORKER_STARTUP_WAIT: 1000,
   PRE_RESTART_SETTLE_DELAY: 2000,  // Give files time to sync before restart

tests/infrastructure/process-manager.test.ts

@@ -1,6 +1,7 @@
 import { describe, it, expect, beforeEach, afterEach } from 'bun:test';
-import { existsSync, readFileSync } from 'fs';
+import { existsSync, readFileSync, mkdirSync, writeFileSync, rmSync } from 'fs';
 import { homedir } from 'os';
+import { tmpdir } from 'os';
 import path from 'path';
 import {
   writePidFile,
@@ -12,6 +13,7 @@ import {
   cleanStalePidFile,
   spawnDaemon,
   resolveWorkerRuntimePath,
+  runOneTimeChromaMigration,
   type PidInfo
 } from '../../src/services/infrastructure/index.js';
 
@@ -32,7 +34,6 @@ describe('ProcessManager', () => {
   afterEach(() => {
     // Restore original PID file or remove test one
     if (originalPidContent !== null) {
-      const { writeFileSync } = require('fs');
       writeFileSync(PID_FILE, originalPidContent);
       originalPidContent = null;
     } else {
@@ -105,7 +106,6 @@ describe('ProcessManager', () => {
     });
 
     it('should return null for corrupted JSON', () => {
-      const { writeFileSync } = require('fs');
       writeFileSync(PID_FILE, 'not valid json {{{');
 
       const result = readPidFile();
@@ -415,4 +415,53 @@ describe('ProcessManager', () => {
       // This is a logic verification test — actual signal delivery is tested manually
     });
   });
+
+  describe('runOneTimeChromaMigration', () => {
+    let testDataDir: string;
+
+    beforeEach(() => {
+      testDataDir = path.join(tmpdir(), `claude-mem-test-${Date.now()}-${Math.random().toString(36).slice(2)}`);
+      mkdirSync(testDataDir, { recursive: true });
+    });
+
+    afterEach(() => {
+      rmSync(testDataDir, { recursive: true, force: true });
+    });
+
+    it('should wipe chroma directory and write marker file', () => {
+      // Create a fake chroma directory with data
+      const chromaDir = path.join(testDataDir, 'chroma');
+      mkdirSync(chromaDir, { recursive: true });
+      writeFileSync(path.join(chromaDir, 'test-data.bin'), 'fake chroma data');
+
+      runOneTimeChromaMigration(testDataDir);
+
+      // Chroma dir should be gone
+      expect(existsSync(chromaDir)).toBe(false);
+      // Marker file should exist
+      expect(existsSync(path.join(testDataDir, '.chroma-cleaned-v10.3'))).toBe(true);
+    });
+
+    it('should skip when marker file already exists (idempotent)', () => {
+      // Write marker file first
+      writeFileSync(path.join(testDataDir, '.chroma-cleaned-v10.3'), 'already done');
+
+      // Create a chroma directory that should NOT be wiped
+      const chromaDir = path.join(testDataDir, 'chroma');
+      mkdirSync(chromaDir, { recursive: true });
+      writeFileSync(path.join(chromaDir, 'important.bin'), 'should survive');
+
+      runOneTimeChromaMigration(testDataDir);
+
+      // Chroma dir should still exist (migration was skipped)
+      expect(existsSync(chromaDir)).toBe(true);
+      expect(existsSync(path.join(chromaDir, 'important.bin'))).toBe(true);
+    });
+
+    it('should handle missing chroma directory gracefully', () => {
+      // No chroma dir exists — should just write marker without error
+      expect(() => runOneTimeChromaMigration(testDataDir)).not.toThrow();
+      expect(existsSync(path.join(testDataDir, '.chroma-cleaned-v10.3'))).toBe(true);
+    });
+  });
 });