beads/docs/TROUBLESHOOTING.md

Troubleshooting bd

Common issues and solutions for bd users.

Table of Contents

• Debug Environment Variables
• Installation Issues
• Antivirus False Positives
• Database Issues
• Git and Sync Issues
• Ready Work and Dependencies
• Performance Issues
• Agent-Specific Issues
• Platform-Specific Issues

Debug Environment Variables

bd supports several environment variables for debugging specific subsystems. Enable these when troubleshooting issues or when requested by maintainers.

Available Debug Variables

Variable	Purpose	Output Location	Usage
BD_DEBUG	General debug logging	stderr	Set to any value to enable
BD_DEBUG_RPC	RPC communication between CLI and daemon	stderr	Set to 1 or true
BD_DEBUG_SYNC	Sync and import timestamp protection	stderr	Set to any value to enable
BD_DEBUG_ROUTING	Issue routing and multi-repo resolution	stderr	Set to any value to enable
BD_DEBUG_FRESHNESS	Database file replacement detection	daemon logs	Set to any value to enable

Usage Examples

General debugging:

# Enable all general debug logging
export BD_DEBUG=1
bd ready

RPC communication issues:

# Debug daemon communication
export BD_DEBUG_RPC=1
bd list

# Example output:
# [RPC DEBUG] Connecting to daemon at .beads/bd.sock
# [RPC DEBUG] Sent request: list (correlation_id=abc123)
# [RPC DEBUG] Received response: 200 OK

Sync conflicts:

# Debug timestamp protection during sync
export BD_DEBUG_SYNC=1
bd sync

# Example output:
# [debug] Protected bd-123: local=2024-01-20T10:00:00Z >= incoming=2024-01-20T09:55:00Z

Routing issues:

# Debug issue routing in multi-repo setups
export BD_DEBUG_ROUTING=1
bd create "Test issue" --rig=planning

# Example output:
# [routing] Rig "planning" -> prefix plan, path /path/to/planning-repo (townRoot=/path/to/town)
# [routing] ID plan-123 matched prefix plan -> /path/to/planning-repo/beads

Database reconnection issues:

# Debug database file replacement detection
export BD_DEBUG_FRESHNESS=1
bd daemon start --foreground

# Example output:
# [freshness] FreshnessChecker: inode changed 27548143 -> 7945906
# [freshness] FreshnessChecker: triggering reconnection
# [freshness] Database file replaced, reconnection triggered

# Or check daemon logs
BD_DEBUG_FRESHNESS=1 bd daemon restart
bd daemons logs . -n 100 | grep freshness

Multiple debug flags:

# Enable multiple subsystems
export BD_DEBUG=1
export BD_DEBUG_RPC=1
export BD_DEBUG_FRESHNESS=1
bd daemon start --foreground

Tips

• Disable after debugging: Debug logging can be verbose. Disable by unsetting the variable:

  unset BD_DEBUG
  unset BD_DEBUG_RPC
  # etc.
  

• Capture debug output: Redirect stderr to a file for analysis:

  BD_DEBUG=1 bd sync 2> debug.log
  

• Daemon logs: BD_DEBUG_FRESHNESS output goes to daemon logs, not stderr:

  # View daemon logs
  bd daemons logs . -n 200
  
  # Or directly:
  tail -f .beads/daemon.log
  

• When filing bug reports: Include relevant debug output to help maintainers diagnose issues faster.

Related Documentation

• DAEMON.md - Daemon management and troubleshooting
• SYNC.md - Git sync behavior and conflict resolution
• ROUTING.md - Multi-repo routing configuration

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

Wrong version of bd running / Multiple bd binaries in PATH

If bd version shows an unexpected version (e.g., older than what you just installed), you likely have multiple bd binaries in your PATH.

Diagnosis:

# Check all bd binaries in PATH
which -a bd

# Example output showing conflict:
# /Users/you/go/bin/bd        <- From go install (older)
# /opt/homebrew/bin/bd        <- From Homebrew (newer)

Solution:

# Remove old go install version
rm ~/go/bin/bd

# Or remove mise-managed Go installs
rm ~/.local/share/mise/installs/go/*/bin/bd

# Verify you're using the correct version
which bd        # Should show /opt/homebrew/bin/bd or your package manager path
bd version      # Should show the expected version

Why this happens: If you previously installed bd via go install, the binary was placed in ~/go/bin/. When you later install via Homebrew or another package manager, the old ~/go/bin/bd may appear earlier in your PATH, causing the wrong version to run.

Recommendation: Choose one installation method (Homebrew recommended) and stick with it. Avoid mixing go install with package managers.

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.

Antivirus False Positives

Antivirus software flags bd as malware

Symptom: Kaspersky, Windows Defender, or other antivirus software detects bd or bd.exe as a trojan or malicious software and removes it.

Common detections:

• Kaspersky: PDM:Trojan.Win32.Generic
• Windows Defender: Various generic trojan detections

Cause: This is a false positive. Go binaries are commonly flagged by antivirus heuristics because some malware is written in Go. This is a known industry-wide issue affecting many legitimate Go projects.

Solutions:

1. Add bd to antivirus exclusions (recommended):

   • Add the bd installation directory to your antivirus exclusion list
   • This is safe - beads is open source and checksums are provided

2. Verify file integrity before excluding:

   # Windows PowerShell
   Get-FileHash bd.exe -Algorithm SHA256
   
   # macOS/Linux
   shasum -a 256 bd
   

   Compare with checksums from the GitHub release page

3. Report the false positive:

   • Help improve detection by reporting to your antivirus vendor
   • Most vendors have false positive submission forms

Detailed guide: See docs/ANTIVIRUS.md for complete instructions including:

• How to add exclusions for specific antivirus software
• How to report false positives to vendors
• Why Go binaries trigger these detections
• Future plans for code signing

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

Import fails with missing parent errors

If you see errors like parent issue bd-abc does not exist when importing hierarchical issues (e.g., bd-abc.1, bd-abc.2), this means the parent issue was deleted but children still reference it.

Quick fix using resurrection:

# Auto-resurrect deleted parents from JSONL history
bd import -i issues.jsonl --orphan-handling resurrect

# Or set as default behavior
bd config set import.orphan_handling "resurrect"
bd sync  # Now uses resurrect mode

What resurrection does:

1. Searches the full JSONL file for the missing parent issue
2. Recreates it as a tombstone (Status=Closed, Priority=4)
3. Preserves the parent's original title and description
4. Maintains referential integrity for hierarchical children
5. Also resurrects dependencies on best-effort basis

Other handling modes:

# Allow orphans (default) - import without validation
bd config set import.orphan_handling "allow"

# Skip orphans - partial import with warnings
bd config set import.orphan_handling "skip"

# Strict - fail fast on missing parents
bd config set import.orphan_handling "strict"

When this happens:

• Parent issue was deleted using bd delete
• Branch merge where one side deleted the parent
• Manual JSONL editing that removed parent entries
• Database corruption or incomplete import

Prevention:

• Use bd delete --cascade to also delete children
• Check for orphans before cleanup: bd list --id bd-abc.*
• Review impact before deleting epic/parent issues

See CONFIG.md for complete configuration documentation.

Old data returns after reset

Symptom: After running bd admin reset --force and bd init, old issues reappear.

Cause: bd admin reset --force only removes local beads data. Old data can return from:

1. Remote sync branch - If you configured a sync branch (via bd init --branch or bd config set sync.branch), old JSONL data may exist on the remote
2. Git history - JSONL files committed to git are preserved in history
3. Other machines - Other clones may push old data after you reset

Solution for complete clean slate:

# 1. Reset local beads
bd admin reset --force

# 2. Delete remote sync branch (if configured)
# Check your sync branch name first:
bd config get sync.branch
# Then delete it from remote:
git push origin --delete <sync-branch-name>
# Common names: beads-sync, beads-metadata

# 3. Remove JSONL from git history (optional, destructive)
# Only do this if you want to completely erase beads history
git filter-branch --force --index-filter \
  'git rm --cached --ignore-unmatch .beads/issues.jsonl' \
  --prune-empty -- --all
git push origin --force --all

# 4. Re-initialize
bd init

Less destructive alternatives:

# Option A: Just delete the sync branch and reinit
bd admin reset --force
git push origin --delete beads-sync  # or your sync branch name
bd init

# Option B: Start fresh without sync branch
bd admin reset --force
bd init
bd config set sync.branch ""  # Disable sync branch feature

Note: The --hard and --skip-init flags mentioned in GH#479 were never implemented. Use the workarounds above for a complete reset.

Related: GH#922

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

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_DIR environment variable to point to your .beads directory if you want to override the default selection
   • Or use BEADS_DB (deprecated) to point directly to the database file

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 .beads directory (recommended)
   BEADS_DIR=/path/to/.beads bd list
   
   # Or add to shell config for permanent override
   export BEADS_DIR=/path/to/.beads
   
   # Legacy method (deprecated, points to database file directly)
   BEADS_DB=/path/to/.beads/issues.db bd list
   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

"Branch already checked out" when switching branches

Symptom:

$ git checkout main
fatal: 'main' is already checked out at '/path/to/.git/beads-worktrees/beads-sync'

Cause: Beads creates git worktrees internally when using the sync-branch feature (configured via bd init --branch or bd config set sync.branch). These worktrees lock the branches they're checked out to.

Solution:

# Remove beads-created worktrees
rm -rf .git/beads-worktrees
rm -rf .git/worktrees/beads-*
git worktree prune

# Now you can checkout the branch
git checkout main

Permanent fix (disable sync-branch):

bd config set sync.branch ""

See WORKTREES.md#beads-created-worktrees-sync-branch for details.

Unexpected worktree directories in .git/

Symptom: You notice .git/beads-worktrees/ or .git/worktrees/beads-* directories you didn't create.

Explanation: Beads automatically creates these worktrees when using the sync-branch feature to commit issue updates to a separate branch without switching your working directory.

If you don't want these:

# Disable sync-branch feature
bd config set sync.branch ""

# Clean up existing worktrees
rm -rf .git/beads-worktrees
rm -rf .git/worktrees/beads-*
git worktree prune

See WORKTREES.md for details on how beads uses worktrees.

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
bd hooks install

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 admin compact --dry-run --all

# Compact old closed issues
bd admin 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 admin 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.

Sandboxed environments (Codex, Claude Code, etc.)

Issue: Sandboxed environments restrict permissions, preventing daemon control and causing "out of sync" errors.

Common symptoms:

• "Database out of sync with JSONL" errors that persist after running bd import
• bd daemon stop fails with "operation not permitted"
• Cannot kill daemon process with kill <pid>
• JSONL hash mismatch warnings (bd-160)
• Commands intermittently fail with staleness errors

Root cause: The sandbox can't signal/kill the existing daemon process, so the DB stays stale and refuses to import.

---

Quick fix: Sandbox mode (auto-detected)

As of v0.21.1+, bd automatically detects sandboxed environments and enables sandbox mode.

When auto-detected, you'll see: ℹ️ Sandbox detected, using direct mode

Manual override (if auto-detection fails):

# Explicitly enable sandbox mode
bd --sandbox ready
bd --sandbox create "Fix bug" -p 1
bd --sandbox update bd-42 --status in_progress

# Equivalent to:
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

---

Escape hatches for stuck states

If you're stuck in a "database out of sync" loop with a running daemon you can't stop, use these flags:

1. Force metadata update (--force flag on import)

When bd import reports "0 created, 0 updated" but staleness persists:

# Force metadata refresh even when DB appears synced
bd import --force

# This updates internal metadata tracking without changing issues
# Fixes: stuck state caused by stale daemon cache

Shows: Metadata updated (database already in sync with JSONL)

2. Skip staleness check (--allow-stale global flag)

Emergency escape hatch to bypass staleness validation:

# Allow operations on potentially stale data
bd --allow-stale ready
bd --allow-stale list --status open

# Shows warning:
# ⚠️  Staleness check skipped (--allow-stale), data may be out of sync

⚠️ Caution: Use sparingly - you may see incomplete or outdated data.

3. Use sandbox mode (preferred)

# Most reliable for sandboxed environments
bd --sandbox ready
bd --sandbox import -i .beads/issues.jsonl

---

Troubleshooting workflow

If stuck in a sandboxed environment:

# Step 1: Try sandbox mode (cleanest solution)
bd --sandbox ready

# Step 2: If you get staleness errors, force import
bd import --force -i .beads/issues.jsonl

# Step 3: If still blocked, use allow-stale (emergency only)
bd --allow-stale ready

# Step 4: When back outside sandbox, sync normally
bd sync

---

Understanding the flags

Flag	Purpose	When to use	Risk
--sandbox	Disable daemon and auto-sync	Sandboxed environments (Codex, containers)	Low - safe for sandboxes
--force (import)	Force metadata update	Stuck "0 created, 0 updated" loop	Low - updates metadata only
--allow-stale	Skip staleness validation	Emergency access to database	High - may show stale data

Related:

• See DAEMON.md for daemon troubleshooting
• See Claude Code sandboxing documentation for more about sandbox restrictions
• GitHub issue #353 for background

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

Windows: Controlled Folder Access blocks bd init

Symptom: bd init hangs indefinitely with high CPU usage, and CTRL+C doesn't work.

Cause: Windows Controlled Folder Access is blocking bd.exe from creating the .beads directory.

Diagnosis: Run with verbose flag to see the actual error:

bd init -v
# Error: failed to create .beads directory: mkdir .beads: The system cannot find the file specified

Solution: Add bd.exe to the Controlled Folder Access whitelist:

1. Open Windows Security → Virus & threat protection
2. Click "Ransomware protection" → "Manage ransomware protection"
3. Under "Controlled folder access", click "Allow an app through Controlled folder access"
4. Click "Add an allowed app" → "Browse all apps"
5. Navigate to and select bd.exe (typically in %USERPROFILE%\go\bin\bd.exe)
6. Retry bd init - it should work instantly

Note: Unlike typical blocked apps, Controlled Folder Access may not show a notification when blocking bd init, making this issue hard to diagnose without the -v flag.

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