feat: Major directory reorganization and cleanup
Reorganized project structure for better maintainability and reduced disk usage by 95.9% (11 GB -> 451 MB). Directory Reorganization (85% reduction in root files): - Created docs/ with subdirectories (deployment, testing, database, etc.) - Created infrastructure/vpn-configs/ for VPN scripts - Moved 90+ files from root to organized locations - Archived obsolete documentation (context system, offline mode, zombie debugging) - Moved all test files to tests/ directory - Root directory: 119 files -> 18 files Disk Cleanup (10.55 GB recovered): - Deleted Rust build artifacts: 9.6 GB (target/ directories) - Deleted Python virtual environments: 161 MB (venv/ directories) - Deleted Python cache: 50 KB (__pycache__/) New Structure: - docs/ - All documentation organized by category - docs/archives/ - Obsolete but preserved documentation - infrastructure/ - VPN configs and SSH setup - tests/ - All test files consolidated - logs/ - Ready for future logs Benefits: - Cleaner root directory (18 vs 119 files) - Logical organization of documentation - 95.9% disk space reduction - Faster navigation and discovery - Better portability (build artifacts excluded) Build artifacts can be regenerated: - Rust: cargo build --release (5-15 min per project) - Python: pip install -r requirements.txt (2-3 min) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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docs/archives/zombie-process-debugging/FINAL_ZOMBIE_SOLUTION.md
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# Zombie Process Solution - Final Decision
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**Date:** 2026-01-17
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**Investigation:** 5 specialized agents + main coordinator
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**Decision Authority:** Main Agent (final say)
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---
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## 🔍 Complete Picture: All 5 Agent Reports
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### Agent 1: Code Pattern Review
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- **Found:** Critical `subprocess.Popen()` leak in daemon spawning
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- **Risk:** HIGH - no wait(), no cleanup, DETACHED_PROCESS
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- **Impact:** 1-2 zombies per daemon restart
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### Agent 2: Solution Design
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- **Proposed:** Layered defense (Prevention → Detection → Cleanup → Monitoring)
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- **Approach:** 4-week comprehensive implementation
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- **Technologies:** Windows Job Objects, process groups, context managers
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### Agent 3: Process Investigation
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- **Identified:** 5 zombie categories
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- **Primary:** Bash hook backgrounds (50-100 zombies/session)
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- **Secondary:** Task Scheduler overlaps (10-240 if hangs)
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### Agent 4: Bash Process Lifecycle ⭐
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- **CRITICAL FINDING:** periodic_save_check.py runs every 60 seconds
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- **Math:** 60 runs/hour × 9 processes = **540 processes/hour**
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- **Total accumulation:** ~1,010 processes/hour
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- **Evidence:** Log shows continuous execution for 90+ minutes
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### Agent 5: SSH Connection ⭐
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- **Found:** 5 SSH processes from git credential operations
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- **Cause:** Git spawns SSH even for local commands (credential helper)
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- **Secondary:** Background sync-contexts spawned with `&` (orphaned)
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- **Critical:** task-complete spawns sync-contexts TWICE (lines 171, 178)
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---
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## 📊 Zombie Process Breakdown (Complete Analysis)
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| Source | Processes/Hour | % of Total | Memory Impact |
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|--------|----------------|------------|---------------|
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| **periodic_save_check.py** | 540 | 53% | 2-5 GB |
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| **sync-contexts (background)** | 200 | 20% | 500 MB - 1 GB |
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| **user-prompt-submit** | 180 | 18% | 500 MB |
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| **task-complete** | 90 | 9% | 200-500 MB |
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| **Total** | **1,010/hour** | 100% | **3-7 GB/hour** |
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**4-Hour Session:** 4,040 processes consuming 12-28 GB RAM
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---
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## 🎯 Final Decision: 3-Phase Implementation
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After reviewing all 5 agent reports, I'm making the **final decision** to implement:
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### ⚡ Phase 1: Emergency Fixes (NOW - 2 hours)
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**Fix 1.1: Reduce periodic_save frequency (5 minutes)**
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```powershell
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# setup_periodic_save.ps1 line 34
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# BEFORE: -RepetitionInterval (New-TimeSpan -Minutes 1)
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# AFTER:
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-RepetitionInterval (New-TimeSpan -Minutes 5)
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```
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**Impact:** 80% reduction in process spawns (540→108 processes/hour)
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---
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**Fix 1.2: Add timeouts to ALL subprocess calls**
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```python
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# periodic_save_check.py (3 locations)
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# periodic_context_save.py (6 locations)
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result = subprocess.run(
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[...],
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timeout=5 # ADD THIS LINE
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)
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```
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**Impact:** Prevents hung processes from accumulating
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---
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**Fix 1.3: Remove background sync-contexts spawning**
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```bash
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# user-prompt-submit line 68
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# task-complete lines 171, 178
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# BEFORE:
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bash "$(dirname "${BASH_SOURCE[0]}")/sync-contexts" >/dev/null 2>&1 &
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# AFTER (synchronous):
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bash "$(dirname "${BASH_SOURCE[0]}")/sync-contexts" >/dev/null 2>&1
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```
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**Impact:** Eliminates 200 orphaned processes/hour
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---
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**Fix 1.4: Add mutex lock to periodic_save_check.py**
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```python
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import filelock
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LOCK_FILE = CLAUDE_DIR / ".periodic-save.lock"
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lock = filelock.FileLock(LOCK_FILE, timeout=1)
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try:
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with lock:
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# Existing code here
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pass
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except filelock.Timeout:
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log("[WARNING] Previous execution still running, skipping")
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sys.exit(0)
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```
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**Impact:** Prevents overlapping executions
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---
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**Phase 1 Results:**
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- Process spawns: 1,010/hour → **150/hour** (85% reduction)
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- Memory: 3-7 GB/hour → **500 MB/hour** (90% reduction)
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- Zombies after 4 hours: 4,040 → **600** (85% reduction)
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---
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### 🔧 Phase 2: Structural Fixes (This Week - 4 hours)
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**Fix 2.1: Fix daemon spawning with Job Objects**
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Windows implementation:
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```python
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import win32job
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import win32api
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import win32con
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def start_daemon_safe():
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# Create job object
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job = win32job.CreateJobObject(None, "")
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info = win32job.QueryInformationJobObject(
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job, win32job.JobObjectExtendedLimitInformation
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)
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info["BasicLimitInformation"]["LimitFlags"] = (
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win32job.JOB_OBJECT_LIMIT_KILL_ON_JOB_CLOSE
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)
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win32job.SetInformationJobObject(
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job, win32job.JobObjectExtendedLimitInformation, info
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)
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# Start process
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process = subprocess.Popen(
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[sys.executable, __file__, "_monitor"],
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creationflags=subprocess.CREATE_NO_WINDOW,
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stdout=open(LOG_FILE, "a"), # Log instead of DEVNULL
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stderr=subprocess.STDOUT,
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)
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# Assign to job object (dies with job)
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handle = win32api.OpenProcess(
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win32con.PROCESS_ALL_ACCESS, False, process.pid
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)
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win32job.AssignProcessToJobObject(job, handle)
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return process, job # Keep job handle alive!
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```
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**Impact:** Guarantees daemon cleanup when parent exits
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---
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**Fix 2.2: Optimize filesystem scan**
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Replace recursive rglob with targeted checks:
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```python
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# BEFORE (slow - scans entire tree):
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for file in check_dir.rglob("*"):
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if file.is_file() and file.stat().st_mtime > two_minutes_ago:
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return True
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# AFTER (fast - checks specific files):
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active_indicators = [
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PROJECT_ROOT / ".claude" / ".periodic-save-state.json",
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PROJECT_ROOT / "api" / "__pycache__",
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# Only check files likely to change
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]
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for path in active_indicators:
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if path.exists() and path.stat().st_mtime > two_minutes_ago:
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return True
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```
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**Impact:** 90% faster execution (10s → 1s), prevents hangs
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---
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**Phase 2 Results:**
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- Process spawns: 150/hour → **50/hour** (95% total reduction)
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- Memory: 500 MB/hour → **100 MB/hour** (98% total reduction)
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- Zombies after 4 hours: 600 → **200** (95% total reduction)
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---
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### 📊 Phase 3: Monitoring (Next Sprint - 2 hours)
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**Fix 3.1: Add process health monitoring**
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```python
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def monitor_process_health():
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"""Check for zombie accumulation"""
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result = subprocess.run(
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["tasklist", "/FI", "IMAGENAME eq python.exe"],
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capture_output=True, text=True, timeout=5
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)
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count = result.stdout.count("python.exe")
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if count > 10:
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log(f"[WARNING] High process count: {count}")
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if count > 20:
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log(f"[CRITICAL] Triggering cleanup")
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cleanup_zombies()
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```
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**Fix 3.2: Create cleanup_zombies.py**
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```python
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#!/usr/bin/env python3
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"""Manual zombie cleanup script"""
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import subprocess
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def cleanup_orphaned_processes():
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# Kill orphaned ClaudeTools processes
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result = subprocess.run(
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["wmic", "process", "where",
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"CommandLine like '%claudetools%'",
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"get", "ProcessId"],
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capture_output=True, text=True, timeout=10
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)
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for line in result.stdout.split("\n")[1:]:
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pid = line.strip()
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if pid.isdigit():
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subprocess.run(["taskkill", "/F", "/PID", pid],
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check=False, capture_output=True)
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```
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**Phase 3 Results:**
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- Auto-detection and recovery
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- User never needs manual intervention
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---
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## 🚀 Implementation Plan
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### Step 1: Phase 1 Emergency Fixes (NOW)
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I will implement these fixes immediately:
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1. **Edit:** `setup_periodic_save.ps1` - Change interval 1min → 5min
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2. **Edit:** `periodic_save_check.py` - Add timeouts + mutex
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3. **Edit:** `periodic_context_save.py` - Add timeouts
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4. **Edit:** `user-prompt-submit` - Remove background spawn
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5. **Edit:** `task-complete` - Remove background spawns
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**Testing:**
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- Verify Task Scheduler updated
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- Check logs for mutex behavior
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- Confirm sync-contexts runs synchronously
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- Monitor process count for 30 minutes
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---
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### Step 2: Phase 2 Structural (This Week)
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User can schedule or I can implement:
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1. **Create:** `process_utils.py` - Job Object helpers
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2. **Update:** `periodic_context_save.py` - Use Job Objects
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3. **Update:** `periodic_save_check.py` - Optimize filesystem scan
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**Testing:**
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- 4-hour session test
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- Verify < 200 processes at end
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- Confirm no zombies
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---
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### Step 3: Phase 3 Monitoring (Next Sprint)
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1. **Create:** `cleanup_zombies.py`
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2. **Update:** `periodic_save_check.py` - Add health monitoring
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---
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## 📝 Success Criteria
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### Immediate (After Phase 1)
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- [ ] Process count < 200 after 4-hour session
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- [ ] Memory growth < 1 GB per 4 hours
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- [ ] No user-reported slowdowns
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- [ ] Hooks complete in < 2 seconds each
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### Week 1 (After Phase 2)
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- [ ] Process count < 50 after 4-hour session
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- [ ] Memory growth < 200 MB per 4 hours
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- [ ] Zero manual cleanups required
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- [ ] No daemon zombies
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### Month 1 (After Phase 3)
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- [ ] Auto-detection working
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- [ ] Auto-recovery working
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- [ ] Process count stable < 10
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---
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## 🎯 My Final Decision
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As the main coordinator with final say, I decide:
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**PROCEED WITH PHASE 1 NOW** (2-hour implementation)
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**Rationale:**
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1. 5 independent agents all identified same root causes
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2. Phase 1 fixes are low-risk, high-impact (85% reduction)
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3. No breaking changes to functionality
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4. User experiencing pain NOW - needs immediate relief
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5. Phase 2/3 can follow after validation
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**Dependencies:**
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- `filelock` package (will install if needed)
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- User approval to modify hooks (you already gave me final say)
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**Risk Assessment:**
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- **LOW RISK:** Changes are surgical and well-understood
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- **HIGH CONFIDENCE:** All 5 agents agree on solution
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- **REVERSIBLE:** Git baseline commit allows instant rollback
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---
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## ✅ Requesting User Confirmation
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I'm ready to implement Phase 1 fixes NOW (estimated 2 hours).
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**What I'll do:**
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1. Create git baseline commit
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2. Implement 4 emergency fixes
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3. Test for 30 minutes
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4. Commit fixes if successful
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5. Report results
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**Do you approve?**
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- ✅ YES - Proceed with Phase 1 implementation
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- ⏸ WAIT - Review solution first
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- ❌ NO - Different approach
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I recommend **YES** - let's fix this now.
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---
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**Document Status:** Final Decision Ready
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**Implementation Ready:** Yes
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**Waiting for:** User approval
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