Claude Threads Debug Skill

Diagnose and troubleshoot issues with claude-threads, orchestrator, threads, worktrees, and agent coordination.

When to Use

Activate this skill when:

Threads are stuck, blocked, or not starting
Orchestrator won't start or crashes
Worktrees are orphaned or inconsistent
Events aren't being delivered
Database is corrupted or inconsistent
Agents aren't coordinating properly
PR lifecycle management isn't working

Quick Diagnostics

System Health Check

bash

# Overall system status
ct orchestrator status
ct api status

# Database integrity
ct db check

# List all threads with status
ct thread list --all

# List worktrees and check for orphans
ct worktree list
ct worktree reconcile

Thread Diagnostics

bash

# Thread status and details
ct thread status <thread-id>
ct thread status <thread-id> --verbose

# Thread logs (last 100 lines)
ct thread logs <thread-id> --tail 100

# Follow logs in real-time
ct thread logs <thread-id> -f

# Find stuck threads
ct thread list blocked
ct thread list running  # Check if actually running

Orchestrator Diagnostics

bash

# Check orchestrator process
ps aux | grep -E "orchestrator|ct"

# Check orchestrator logs
cat .claude-threads/logs/orchestrator.log | tail -100

# Check for lock files
ls -la .claude-threads/*.lock 2>/dev/null

# Remove stale lock (if orchestrator crashed)
rm -f .claude-threads/orchestrator.lock

Worktree Diagnostics

bash

# List all worktrees
ct worktree list

# Check for orphaned worktrees
ct worktree reconcile

# Auto-fix orphaned worktrees
ct worktree reconcile --fix

# Check git worktree status directly
git worktree list

# Check specific worktree
ct worktree status <worktree-id>

Base + Fork Diagnostics

bash

# List base worktrees
sqlite3 .claude-threads/threads.db "SELECT * FROM pr_base_worktrees;"

# List forks
sqlite3 .claude-threads/threads.db "SELECT * FROM pr_worktree_forks;"

# Check base status for a PR
ct worktree base-status <pr-number>

# List forks for a PR
ct worktree list-forks <pr-number>

# Check for stale locks
ls -la .claude-threads/worktrees/*.lock 2>/dev/null

Event Diagnostics

bash

# List recent events
ct event list --limit 50

# Filter by type
ct event list --type THREAD_FAILED --limit 20
ct event list --type ESCALATION_NEEDED --limit 20

# Filter by source
ct event list --source <thread-id> --limit 20

# Watch events in real-time
ct event watch --types "FAILED,BLOCKED,ESCALATION"

Database Diagnostics

bash

# Check database file
ls -la .claude-threads/threads.db

# Check database integrity
sqlite3 .claude-threads/threads.db "PRAGMA integrity_check;"

# Check schema version
sqlite3 .claude-threads/threads.db "SELECT * FROM schema_migrations ORDER BY version DESC LIMIT 5;"

# Count records
sqlite3 .claude-threads/threads.db "
SELECT 'threads' as table_name, COUNT(*) as count FROM threads
UNION ALL
SELECT 'events', COUNT(*) FROM events
UNION ALL
SELECT 'pr_watches', COUNT(*) FROM pr_watches
UNION ALL
SELECT 'pr_base_worktrees', COUNT(*) FROM pr_base_worktrees
UNION ALL
SELECT 'pr_worktree_forks', COUNT(*) FROM pr_worktree_forks;
"

# Find threads in bad state
sqlite3 .claude-threads/threads.db "
SELECT id, name, status, updated_at
FROM threads
WHERE status IN ('blocked', 'failed', 'error')
ORDER BY updated_at DESC;
"

API Diagnostics

bash

# Check API health
curl -s http://localhost:31337/api/health | jq .

# Check API status
curl -s http://localhost:31337/api/status | jq .

# Check with auth
curl -s -H "Authorization: Bearer $CT_API_TOKEN" \
  http://localhost:31337/api/status | jq .

# Check API process
lsof -i :31337

PR Shepherd Diagnostics

bash

# List watched PRs
ct pr list

# Check specific PR status
ct pr status <pr-number>

# Check PR comments
ct pr comments <pr-number>

# Check PR conflicts
ct pr conflicts <pr-number>

# Check PR shepherd logs
cat .claude-threads/logs/pr-shepherd.log | tail -100

Common Issues and Fixes

Issue: Thread Stuck in "running" but not executing

Symptoms:

Thread shows "running" in ct thread list
No activity in logs
Process may have crashed

Diagnosis:

bash

ct thread status <thread-id> --verbose
ps aux | grep <thread-id>
cat .claude-threads/logs/thread-<thread-id>.log | tail -50

Fix:

bash

# Force stop and restart
ct thread stop <thread-id> --force
ct thread start <thread-id>

Issue: Orchestrator won't start

Symptoms:

ct orchestrator start hangs or fails
"Already running" but no process

Diagnosis:

bash

ls -la .claude-threads/orchestrator.lock
ps aux | grep orchestrator

Fix:

bash

# Remove stale lock
rm -f .claude-threads/orchestrator.lock
ct orchestrator start

Issue: Worktrees out of sync with database

Symptoms:

Worktrees exist on disk but not in database (or vice versa)
Fork operations fail

Diagnosis:

bash

ct worktree reconcile

Fix:

bash

ct worktree reconcile --fix

Issue: Fork merge-back fails

Symptoms:

ct worktree merge-back returns error
Conflict during merge

Diagnosis:

bash

cd $(ct worktree fork-path <fork-id>)
git status
git diff

Fix:

bash

# Option 1: Retry with updated base
ct worktree remove-fork <fork-id> --force
ct worktree base-update <pr-number>
# Re-fork and retry

# Option 2: Manual merge
cd $(ct worktree base-path <pr-number>)
git merge --no-commit $(ct worktree fork-path <fork-id>)
# Resolve conflicts manually
git add .
git commit -m "Merge fork with manual conflict resolution"
ct worktree remove-fork <fork-id> --force

Issue: Events not being delivered

Symptoms:

Agent publishes event but listener never receives
Events stuck in queue

Diagnosis:

bash

ct event list --limit 50
sqlite3 .claude-threads/threads.db "
SELECT type, COUNT(*), MAX(created_at)
FROM events
GROUP BY type
ORDER BY MAX(created_at) DESC;
"

Fix:

bash

# Check if event TTL is too short
cat .claude-threads/config.yaml | grep -A5 events

# Manually trigger event processing
ct event process

Issue: Database locked

Symptoms:

"database is locked" errors
Operations fail intermittently

Diagnosis:

bash

lsof .claude-threads/threads.db

Fix:

bash

# Stop all threads and orchestrator
ct orchestrator stop
ct thread list running | xargs -I {} ct thread stop {}

# Wait for locks to release
sleep 5

# Restart
ct orchestrator start

Issue: API returns 401/403

Symptoms:

Remote connections fail with auth errors
"Unauthorized" responses

Diagnosis:

bash

# Check token configuration
grep api_token .claude-threads/config.yaml
echo $CT_API_TOKEN
echo $N8N_API_TOKEN

# Test with token
curl -v -H "Authorization: Bearer $CT_API_TOKEN" \
  http://localhost:31337/api/health

Fix:

bash

# Reconnect with correct token
ct remote disconnect
ct remote connect localhost:31337 --token $CT_API_TOKEN

Advanced Debugging

Enable Verbose Logging

bash

# Set debug mode
export CT_DEBUG=1
export CT_LOG_LEVEL=debug

# Restart orchestrator with debug
ct orchestrator restart

Trace Event Flow

bash

# Watch all events
ct event watch

# In another terminal, trigger action and observe
ct spawn test-thread --template developer.md

Database Queries

bash

# Find all threads for a PR
sqlite3 .claude-threads/threads.db "
SELECT t.id, t.name, t.status, t.created_at
FROM threads t
WHERE t.context LIKE '%\"pr_number\":123%'
ORDER BY t.created_at DESC;
"

# Find recent failures
sqlite3 .claude-threads/threads.db "
SELECT id, name, status, error_message, updated_at
FROM threads
WHERE status = 'failed'
ORDER BY updated_at DESC
LIMIT 10;
"

# Check event delivery
sqlite3 .claude-threads/threads.db "
SELECT e.type, e.source_thread_id, e.created_at,
       substr(e.data, 1, 100) as data_preview
FROM events e
ORDER BY e.created_at DESC
LIMIT 20;
"

Process Tracing

bash

# Find all claude-threads related processes
ps aux | grep -E "ct|claude|orchestrator" | grep -v grep

# Check process tree
pstree -p $(pgrep -f orchestrator)

# Check file descriptors
lsof -p $(pgrep -f orchestrator)

Git State Recovery

bash

# If worktree is corrupted
cd .claude-threads/worktrees/<worktree-id>
git fsck
git gc --prune=now

# Remove and recreate worktree
git worktree remove .claude-threads/worktrees/<worktree-id> --force
ct worktree cleanup

Cleanup Commands

bash

# Stop everything
ct orchestrator stop
ct api stop

# Clean up all threads
ct thread list --all | xargs -I {} ct thread delete {}

# Clean up all worktrees
ct worktree cleanup --force

# Clean up orphaned forks
ct worktree reconcile --fix

# Reset database (DESTRUCTIVE)
rm .claude-threads/threads.db
ct db migrate

# Full reset (DESTRUCTIVE)
rm -rf .claude-threads
ct init

Documentation

ARCHITECTURE.md - System architecture
AGENT-COORDINATION.md - Agent coordination
WORKTREE-GUIDE.md - Worktree management
EVENT-REFERENCE.md - Event types

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SKILL.md

Claude Threads Debug Skill

When to Use

Quick Diagnostics

System Health Check

Thread Diagnostics

Orchestrator Diagnostics

Worktree Diagnostics

Base + Fork Diagnostics

Event Diagnostics

Database Diagnostics

API Diagnostics

PR Shepherd Diagnostics

Common Issues and Fixes

Issue: Thread Stuck in "running" but not executing

Issue: Orchestrator won't start

Issue: Worktrees out of sync with database

Issue: Fork merge-back fails

Issue: Events not being delivered

Issue: Database locked

Issue: API returns 401/403

Advanced Debugging

Enable Verbose Logging

Trace Event Flow

Database Queries

Process Tracing

Git State Recovery

Cleanup Commands

Documentation