beads/TROUBLESHOOTING.md

Troubleshooting bd

Common issues and solutions for bd users.

Table of Contents

• Installation Issues
• Database Issues
• Git and Sync Issues
• Ready Work and Dependencies
• Performance Issues
• Agent-Specific Issues
• Platform-Specific Issues

Installation Issues

bd: command not found

bd is not in your PATH. Either:

# Check if installed
go list -f {{.Target}} github.com/steveyegge/beads/cmd/bd

# Add Go bin to PATH (add to ~/.bashrc or ~/.zshrc)
export PATH="$PATH:$(go env GOPATH)/bin"

# Or reinstall
go install github.com/steveyegge/beads/cmd/bd@latest

zsh: killed bd or crashes on macOS

Some users report crashes when running bd init or other commands on macOS. This is typically caused by CGO/SQLite compatibility issues.

Workaround:

# Build with CGO enabled
CGO_ENABLED=1 go install github.com/steveyegge/beads/cmd/bd@latest

# Or if building from source
git clone https://github.com/steveyegge/beads
cd beads
CGO_ENABLED=1 go build -o bd ./cmd/bd
sudo mv bd /usr/local/bin/

If you installed via Homebrew, this shouldn't be necessary as the formula already enables CGO. If you're still seeing crashes with the Homebrew version, please file an issue.

Database Issues

database is locked

Another bd process is accessing the database, or SQLite didn't close properly. Solutions:

# Find and kill hanging processes
ps aux | grep bd
kill <pid>

# Remove lock files (safe if no bd processes running)
rm .beads/*.db-journal .beads/*.db-wal .beads/*.db-shm

Note: bd uses a pure Go SQLite driver (modernc.org/sqlite) for better portability. Under extreme concurrent load (100+ simultaneous operations), you may see "database is locked" errors. This is a known limitation of the pure Go implementation and does not affect normal usage. For very high concurrency scenarios, consider using the CGO-enabled driver or PostgreSQL (planned for future release).

bd init fails with "directory not empty"

.beads/ already exists. Options:

# Use existing database
bd list  # Should work if already initialized

# Or remove and reinitialize (DESTROYS DATA!)
rm -rf .beads/
bd init

failed to import: issue already exists

You're trying to import issues that conflict with existing ones. Options:

# Skip existing issues (only import new ones)
bd import -i issues.jsonl --skip-existing

# Or clear database and re-import everything
rm .beads/*.db
bd import -i .beads/issues.jsonl

Database corruption

Important: Distinguish between logical consistency issues (ID collisions, wrong prefixes) and physical SQLite corruption.

For physical database corruption (disk failures, power loss, filesystem errors):

# Check database integrity
sqlite3 .beads/*.db "PRAGMA integrity_check;"

# If corrupted, reimport from JSONL (source of truth in git)
mv .beads/*.db .beads/*.db.backup
bd init
bd import -i .beads/issues.jsonl

For logical consistency issues (ID collisions from branch merges, parallel workers):

# This is NOT corruption - use collision resolution instead
bd import -i .beads/issues.jsonl --resolve-collisions

See FAQ for the distinction.

Multiple databases detected warning

If you see a warning about multiple .beads databases in the directory hierarchy:

╔══════════════════════════════════════════════════════════════════════════╗
║ WARNING: 2 beads databases detected in directory hierarchy             ║
╠══════════════════════════════════════════════════════════════════════════╣
║ Multiple databases can cause confusion and database pollution.          ║
║                                                                          ║
║ ▶ /path/to/project/.beads (15 issues)                                   ║
║   /path/to/parent/.beads (32 issues)                                    ║
║                                                                          ║
║ Currently using the closest database (▶). This is usually correct.      ║
║                                                                          ║
║ RECOMMENDED: Consolidate or remove unused databases to avoid confusion. ║
╚══════════════════════════════════════════════════════════════════════════╝

This means bd found multiple .beads directories in your directory hierarchy. The ▶ marker shows which database is actively being used (usually the closest one to your current directory).

Why this matters:

• Can cause confusion about which database contains your work
• Easy to accidentally work in the wrong database
• May lead to duplicate tracking of the same work

Solutions:

1. If you have nested projects (intentional):

   • This is fine! bd is designed to support this
   • Just be aware which database you're using
   • Set BEADS_DB environment variable if you want to override the default selection

2. If you have accidental duplicates (unintentional):

   • Decide which database to keep
   • Export issues from the unwanted database: cd <unwanted-dir> && bd export -o backup.jsonl
   • Remove the unwanted .beads directory: rm -rf <unwanted-dir>/.beads
   • Optionally import issues into the main database if needed

3. Override database selection:

   # Temporarily use specific database
   BEADS_DB=/path/to/.beads/issues.db bd list
   
   # Or add to shell config for permanent override
   export BEADS_DB=/path/to/.beads/issues.db
   

Note: The warning only appears when bd detects multiple databases. If you see this consistently and want to suppress it, you're using the correct database (marked with ▶).

Git and Sync Issues

Git merge conflict in issues.jsonl

When both sides add issues, you'll get conflicts. Resolution:

1. Open .beads/issues.jsonl
2. Look for <<<<<<< HEAD markers
3. Most conflicts can be resolved by keeping both sides
4. Each line is independent unless IDs conflict
5. For same-ID conflicts, keep the newest (check updated_at)

Example resolution:

# After resolving conflicts manually
git add .beads/issues.jsonl
git commit
bd import -i .beads/issues.jsonl  # Sync to SQLite

See ADVANCED.md for detailed merge strategies.

Git merge conflicts in JSONL

With hash-based IDs (v0.20.1+), ID collisions don't occur. Different issues get different hash IDs.

If git shows a conflict in .beads/issues.jsonl, it's because the same issue was modified on both branches:

# Preview what will be updated
bd import -i .beads/issues.jsonl --dry-run

# Resolve git conflict (keep newer version or manually merge)
git checkout --theirs .beads/issues.jsonl  # Or --ours, or edit manually

# Import updates the database
bd import -i .beads/issues.jsonl

See ADVANCED.md#handling-git-merge-conflicts for details.

Permission denied on git hooks

Git hooks need execute permissions:

chmod +x .git/hooks/pre-commit
chmod +x .git/hooks/post-merge
chmod +x .git/hooks/post-checkout

Or use the installer: cd examples/git-hooks && ./install.sh

Auto-sync not working

Check if auto-sync is enabled:

# Check if daemon is running
ps aux | grep "bd daemon"

# Manually export/import
bd export -o .beads/issues.jsonl
bd import -i .beads/issues.jsonl

# Install git hooks for guaranteed sync
cd examples/git-hooks && ./install.sh

If you disabled auto-sync with --no-auto-flush or --no-auto-import, remove those flags or use bd sync manually.

Ready Work and Dependencies

bd ready shows nothing but I have open issues

Those issues probably have open blockers. Check:

# See blocked issues
bd blocked

# Show dependency tree (default max depth: 50)
bd dep tree <issue-id>

# Limit tree depth to prevent deep traversals
bd dep tree <issue-id> --max-depth 10

# Remove blocking dependency if needed
bd dep remove <from-id> <to-id>

Remember: Only blocks dependencies affect ready work.

Circular dependency errors

bd prevents dependency cycles, which break ready work detection. To fix:

# Detect all cycles
bd dep cycles

# Remove the dependency causing the cycle
bd dep remove <from-id> <to-id>

# Or redesign your dependency structure

Dependencies not showing up

Check the dependency type:

# Show full issue details including dependencies
bd show <issue-id>

# Visualize the dependency tree
bd dep tree <issue-id>

Remember: Different dependency types have different meanings:

• blocks - Hard blocker, affects ready work
• related - Soft relationship, doesn't block
• parent-child - Hierarchical (child depends on parent)
• discovered-from - Work discovered during another issue

Performance Issues

Export/import is slow

For large databases (10k+ issues):

# Export only open issues
bd export --format=jsonl --status=open -o .beads/issues.jsonl

# Or filter by priority
bd export --format=jsonl --priority=0 --priority=1 -o critical.jsonl

Consider splitting large projects into multiple databases.

Commands are slow

Check database size and consider compaction:

# Check database stats
bd stats

# Preview compaction candidates
bd compact --dry-run --all

# Compact old closed issues
bd compact --days 90

Large JSONL files

If .beads/issues.jsonl is very large:

# Check file size
ls -lh .beads/issues.jsonl

# Remove old closed issues
bd compact --days 90

# Or split into multiple projects
cd ~/project/component1 && bd init --prefix comp1
cd ~/project/component2 && bd init --prefix comp2

Agent-Specific Issues

Agent creates duplicate issues

Agents may not realize an issue already exists. Prevention strategies:

• Have agents search first: bd list --json | grep "title"
• Use labels to mark auto-created issues: bd create "..." -l auto-generated
• Review and deduplicate periodically: bd list | sort
• Use bd merge to consolidate duplicates: bd merge bd-2 --into bd-1

Agent gets confused by complex dependencies

Simplify the dependency structure:

# Check for overly complex trees
bd dep tree <issue-id>

# Remove unnecessary dependencies
bd dep remove <from-id> <to-id>

# Use labels instead of dependencies for loose relationships
bd label add <issue-id> related-to-feature-X

Agent can't find ready work

Check if issues are blocked:

# See what's blocked
bd blocked

# See what's actually ready
bd ready --json

# Check specific issue
bd show <issue-id>
bd dep tree <issue-id>

MCP server not working

Check installation and configuration:

# Verify MCP server is installed
pip list | grep beads-mcp

# Check MCP configuration
cat ~/Library/Application\ Support/Claude/claude_desktop_config.json

# Test CLI works
bd version
bd ready

# Check for daemon
ps aux | grep "bd daemon"

See integrations/beads-mcp/README.md for MCP-specific troubleshooting.

Claude Code sandbox mode

Issue: Claude Code's sandbox restricts network access to a single socket, conflicting with bd's daemon and git operations.

Solution: Use the --sandbox flag:

# Sandbox mode disables daemon and auto-sync
bd --sandbox ready
bd --sandbox create "Fix bug" -p 1
bd --sandbox update bd-42 --status in_progress

# Or set individual flags
bd --no-daemon --no-auto-flush --no-auto-import <command>

What sandbox mode does:

• Disables daemon (uses direct SQLite mode)
• Disables auto-export to JSONL
• Disables auto-import from JSONL
• Allows bd to work in network-restricted environments

Note: You'll need to manually sync when outside the sandbox:

# After leaving sandbox, sync manually
bd sync

Related: See Claude Code sandboxing documentation for more about sandbox restrictions.

Platform-Specific Issues

Windows: Path issues

# Check if bd.exe is in PATH
where.exe bd

# Add Go bin to PATH (permanently)
[Environment]::SetEnvironmentVariable(
    "Path",
    $env:Path + ";$env:USERPROFILE\go\bin",
    [EnvironmentVariableTarget]::User
)

# Reload PATH in current session
$env:Path = [Environment]::GetEnvironmentVariable("Path", "User")

Windows: Firewall blocking daemon

The daemon listens on loopback TCP. Allow bd.exe through Windows Firewall:

1. Open Windows Security → Firewall & network protection
2. Click "Allow an app through firewall"
3. Add bd.exe and enable for Private networks
4. Or disable firewall temporarily for testing

macOS: Gatekeeper blocking execution

If macOS blocks bd:

# Remove quarantine attribute
xattr -d com.apple.quarantine /usr/local/bin/bd

# Or allow in System Preferences
# System Preferences → Security & Privacy → General → "Allow anyway"

Linux: Permission denied

If you get permission errors:

# Make bd executable
chmod +x /usr/local/bin/bd

# Or install to user directory
mkdir -p ~/.local/bin
mv bd ~/.local/bin/
export PATH="$HOME/.local/bin:$PATH"

Getting Help

If none of these solutions work:

1. Check existing issues: GitHub Issues
2. Enable debug logging: bd --verbose <command>
3. File a bug report: Include:
   • bd version: bd version
   • OS and architecture: uname -a
   • Error message and full command
   • Steps to reproduce
4. Join discussions: GitHub Discussions

Related Documentation

• README.md - Core features and quick start
• ADVANCED.md - Advanced features
• FAQ.md - Frequently asked questions
• INSTALLING.md - Installation guide
• ADVANCED.md - JSONL format and merge strategies