panopticon-cli 0.4.6 → 0.4.7

package/skills/beads/resources/CLI_REFERENCE.md

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+# CLI Command Reference
+
+**For:** AI agents and developers using bd command-line interface
+**Version:** 0.21.0+
+
+## Quick Navigation
+
+- [Basic Operations](#basic-operations)
+- [Issue Management](#issue-management)
+- [Dependencies & Labels](#dependencies--labels)
+- [Filtering & Search](#filtering--search)
+- [Advanced Operations](#advanced-operations)
+- [Database Management](#database-management)
+
+## Basic Operations
+
+### Check Status
+
+```bash
+# Check database path and daemon status
+bd info --json
+
+# Example output:
+# {
+#   "database_path": "/path/to/.beads/beads.db",
+#   "issue_prefix": "bd",
+#   "daemon_running": true
+# }
+```
+
+### Find Work
+
+```bash
+# Find ready work (no blockers)
+bd ready --json
+
+# Find stale issues (not updated recently)
+bd stale --days 30 --json                    # Default: 30 days
+bd stale --days 90 --status in_progress --json  # Filter by status
+bd stale --limit 20 --json                   # Limit results
+```
+
+## Issue Management
+
+### Create Issues
+
+```bash
+# Basic creation
+# IMPORTANT: Always quote titles and descriptions with double quotes
+bd create "Issue title" -t bug|feature|task -p 0-4 -d "Description" --json
+
+# Create with explicit ID (for parallel workers)
+bd create "Issue title" --id worker1-100 -p 1 --json
+
+# Create with labels (--labels or --label work)
+bd create "Issue title" -t bug -p 1 -l bug,critical --json
+bd create "Issue title" -t bug -p 1 --label bug,critical --json
+
+# Examples with special characters (all require quoting):
+bd create "Fix: auth doesn't validate tokens" -t bug -p 1 --json
+bd create "Add support for OAuth 2.0" -d "Implement RFC 6749 (OAuth 2.0 spec)" --json
+
+# Create multiple issues from markdown file
+bd create -f feature-plan.md --json
+
+# Create epic with hierarchical child tasks
+bd create "Auth System" -t epic -p 1 --json         # Returns: bd-a3f8e9
+bd create "Login UI" -p 1 --json                     # Auto-assigned: bd-a3f8e9.1
+bd create "Backend validation" -p 1 --json           # Auto-assigned: bd-a3f8e9.2
+bd create "Tests" -p 1 --json                        # Auto-assigned: bd-a3f8e9.3
+
+# Create and link discovered work (one command)
+bd create "Found bug" -t bug -p 1 --deps discovered-from:<parent-id> --json
+```
+
+### Update Issues
+
+```bash
+# Update one or more issues
+bd update <id> [<id>...] --status in_progress --json
+bd update <id> [<id>...] --priority 1 --json
+
+# Edit issue fields in $EDITOR (HUMANS ONLY - not for agents)
+# NOTE: This command is intentionally NOT exposed via the MCP server
+# Agents should use 'bd update' with field-specific parameters instead
+bd edit <id>                    # Edit description
+bd edit <id> --title            # Edit title
+bd edit <id> --design           # Edit design notes
+bd edit <id> --notes            # Edit notes
+bd edit <id> --acceptance       # Edit acceptance criteria
+```
+
+### Close/Reopen Issues
+
+```bash
+# Complete work (supports multiple IDs)
+bd close <id> [<id>...] --reason "Done" --json
+
+# Reopen closed issues (supports multiple IDs)
+bd reopen <id> [<id>...] --reason "Reopening" --json
+```
+
+### View Issues
+
+```bash
+# Show dependency tree
+bd dep tree <id>
+
+# Get issue details (supports multiple IDs)
+bd show <id> [<id>...] --json
+```
+
+## Dependencies & Labels
+
+### Dependencies
+
+```bash
+# Link discovered work (old way - two commands)
+bd dep add <discovered-id> <parent-id> --type discovered-from
+
+# Create and link in one command (new way - preferred)
+bd create "Issue title" -t bug -p 1 --deps discovered-from:<parent-id> --json
+```
+
+### Labels
+
+```bash
+# Label management (supports multiple IDs)
+bd label add <id> [<id>...] <label> --json
+bd label remove <id> [<id>...] <label> --json
+bd label list <id> --json
+bd label list-all --json
+```
+
+## Filtering & Search
+
+### Basic Filters
+
+```bash
+# Filter by status, priority, type
+bd list --status open --priority 1 --json               # Status and priority
+bd list --assignee alice --json                         # By assignee
+bd list --type bug --json                               # By issue type
+bd list --id bd-123,bd-456 --json                       # Specific IDs
+```
+
+### Label Filters
+
+```bash
+# Labels (AND: must have ALL)
+bd list --label bug,critical --json
+
+# Labels (OR: has ANY)
+bd list --label-any frontend,backend --json
+```
+
+### Text Search
+
+```bash
+# Title search (substring)
+bd list --title "auth" --json
+
+# Pattern matching (case-insensitive substring)
+bd list --title-contains "auth" --json                  # Search in title
+bd list --desc-contains "implement" --json              # Search in description
+bd list --notes-contains "TODO" --json                  # Search in notes
+```
+
+### Date Range Filters
+
+```bash
+# Date range filters (YYYY-MM-DD or RFC3339)
+bd list --created-after 2024-01-01 --json               # Created after date
+bd list --created-before 2024-12-31 --json              # Created before date
+bd list --updated-after 2024-06-01 --json               # Updated after date
+bd list --updated-before 2024-12-31 --json              # Updated before date
+bd list --closed-after 2024-01-01 --json                # Closed after date
+bd list --closed-before 2024-12-31 --json               # Closed before date
+```
+
+### Empty/Null Checks
+
+```bash
+# Empty/null checks
+bd list --empty-description --json                      # Issues with no description
+bd list --no-assignee --json                            # Unassigned issues
+bd list --no-labels --json                              # Issues with no labels
+```
+
+### Priority Ranges
+
+```bash
+# Priority ranges
+bd list --priority-min 0 --priority-max 1 --json        # P0 and P1 only
+bd list --priority-min 2 --json                         # P2 and below
+```
+
+### Combine Filters
+
+```bash
+# Combine multiple filters
+bd list --status open --priority 1 --label-any urgent,critical --no-assignee --json
+```
+
+## Global Flags
+
+Global flags work with any bd command and must appear **before** the subcommand.
+
+### Sandbox Mode
+
+**Auto-detection (v0.21.1+):** bd automatically detects sandboxed environments and enables sandbox mode.
+
+When detected, you'll see: `ℹ️  Sandbox detected, using direct mode`
+
+**Manual override:**
+
+```bash
+# Explicitly enable sandbox mode
+bd --sandbox <command>
+
+# Equivalent to combining these flags:
+bd --no-daemon --no-auto-flush --no-auto-import <command>
+```
+
+**What it does:**
+- Disables daemon (uses direct SQLite mode)
+- Disables auto-export to JSONL
+- Disables auto-import from JSONL
+
+**When to use:** Sandboxed environments where daemon can't be controlled (permission restrictions), or when auto-detection doesn't trigger.
+
+### Staleness Control
+
+```bash
+# Skip staleness check (emergency escape hatch)
+bd --allow-stale <command>
+
+# Example: access database even if out of sync with JSONL
+bd --allow-stale ready --json
+bd --allow-stale list --status open --json
+```
+
+**Shows:** `⚠️  Staleness check skipped (--allow-stale), data may be out of sync`
+
+**⚠️ Caution:** May show stale or incomplete data. Use only when stuck and other options fail.
+
+### Force Import
+
+```bash
+# Force metadata update even when DB appears synced
+bd import --force -i .beads/issues.jsonl
+```
+
+**When to use:** `bd import` reports "0 created, 0 updated" but staleness errors persist.
+
+**Shows:** `Metadata updated (database already in sync with JSONL)`
+
+### Other Global Flags
+
+```bash
+# JSON output for programmatic use
+bd --json <command>
+
+# Force direct mode (bypass daemon)
+bd --no-daemon <command>
+
+# Disable auto-sync
+bd --no-auto-flush <command>    # Disable auto-export to JSONL
+bd --no-auto-import <command>   # Disable auto-import from JSONL
+
+# Custom database path
+bd --db /path/to/.beads/beads.db <command>
+
+# Custom actor for audit trail
+bd --actor alice <command>
+```
+
+**See also:**
+- [TROUBLESHOOTING.md - Sandboxed environments](TROUBLESHOOTING.md#sandboxed-environments-codex-claude-code-etc) for detailed sandbox troubleshooting
+- [DAEMON.md](DAEMON.md) for daemon mode details
+
+## Advanced Operations
+
+### Cleanup
+
+```bash
+# Clean up closed issues (bulk deletion)
+bd admin cleanup --force --json                                   # Delete ALL closed issues
+bd admin cleanup --older-than 30 --force --json                   # Delete closed >30 days ago
+bd admin cleanup --dry-run --json                                 # Preview what would be deleted
+bd admin cleanup --older-than 90 --cascade --force --json         # Delete old + dependents
+```
+
+### Duplicate Detection & Merging
+
+```bash
+# Find and merge duplicate issues
+bd duplicates                                          # Show all duplicates
+bd duplicates --auto-merge                             # Automatically merge all
+bd duplicates --dry-run                                # Preview merge operations
+
+# Merge specific duplicate issues
+bd merge <source-id...> --into <target-id> --json      # Consolidate duplicates
+bd merge bd-42 bd-43 --into bd-41 --dry-run            # Preview merge
+```
+
+### Compaction (Memory Decay)
+
+```bash
+# Agent-driven compaction
+bd admin compact --analyze --json                           # Get candidates for review
+bd admin compact --analyze --tier 1 --limit 10 --json       # Limited batch
+bd admin compact --apply --id bd-42 --summary summary.txt   # Apply compaction
+bd admin compact --apply --id bd-42 --summary - < summary.txt  # From stdin
+bd admin compact --stats --json                             # Show statistics
+
+# Legacy AI-powered compaction (requires ANTHROPIC_API_KEY)
+bd admin compact --auto --dry-run --all                     # Preview
+bd admin compact --auto --all --tier 1                      # Auto-compact tier 1
+
+# Restore compacted issue from git history
+bd restore <id>  # View full history at time of compaction
+```
+
+### Rename Prefix
+
+```bash
+# Rename issue prefix (e.g., from 'knowledge-work-' to 'kw-')
+bd rename-prefix kw- --dry-run  # Preview changes
+bd rename-prefix kw- --json     # Apply rename
+```
+
+## Database Management
+
+### Import/Export
+
+```bash
+# Import issues from JSONL
+bd import -i .beads/issues.jsonl --dry-run      # Preview changes
+bd import -i .beads/issues.jsonl                # Import and update issues
+bd import -i .beads/issues.jsonl --dedupe-after # Import + detect duplicates
+
+# Handle missing parents during import
+bd import -i issues.jsonl --orphan-handling allow      # Default: import orphans without validation
+bd import -i issues.jsonl --orphan-handling resurrect  # Auto-resurrect deleted parents as tombstones
+bd import -i issues.jsonl --orphan-handling skip       # Skip orphans with warning
+bd import -i issues.jsonl --orphan-handling strict     # Fail if parent is missing
+
+# Configure default orphan handling behavior
+bd config set import.orphan_handling "resurrect"
+bd sync  # Now uses resurrect mode by default
+```
+
+**Orphan handling modes:**
+
+- **`allow` (default)** - Import orphaned children without parent validation. Most permissive, ensures no data loss even if hierarchy is temporarily broken.
+- **`resurrect`** - Search JSONL history for deleted parents and recreate them as tombstones (Status=Closed, Priority=4). Preserves hierarchy with minimal data. Dependencies are also resurrected on best-effort basis.
+- **`skip`** - Skip orphaned children with warning. Partial import succeeds but some issues are excluded.
+- **`strict`** - Fail import immediately if a child's parent is missing. Use when database integrity is critical.
+
+**When to use:**
+- Use `allow` (default) for daily imports and auto-sync
+- Use `resurrect` when importing from databases with deleted parents
+- Use `strict` for controlled imports requiring guaranteed parent existence
+- Use `skip` rarely - only for selective imports
+
+See [CONFIG.md](CONFIG.md#example-import-orphan-handling) and [TROUBLESHOOTING.md](TROUBLESHOOTING.md#import-fails-with-missing-parent-errors) for more details.
+
+### Migration
+
+```bash
+# Migrate databases after version upgrade
+bd migrate                                             # Detect and migrate old databases
+bd migrate --dry-run                                   # Preview migration
+bd migrate --cleanup --yes                             # Migrate and remove old files
+
+# AI-supervised migration (check before running bd migrate)
+bd migrate --inspect --json                            # Show migration plan for AI agents
+bd info --schema --json                                # Get schema, tables, config, sample IDs
+```
+
+**Migration workflow for AI agents:**
+
+1. Run `--inspect` to see pending migrations and warnings
+2. Check for `missing_config` (like issue_prefix)
+3. Review `invariants_to_check` for safety guarantees
+4. If warnings exist, fix config issues first
+5. Then run `bd migrate` safely
+
+**Migration safety invariants:**
+
+- **required_config_present**: Ensures issue_prefix and schema_version are set
+- **foreign_keys_valid**: No orphaned dependencies or labels
+- **issue_count_stable**: Issue count doesn't decrease unexpectedly
+
+These invariants prevent data loss and would have caught issues like GH #201 (missing issue_prefix after migration).
+
+### Daemon Management
+
+See [docs/DAEMON.md](DAEMON.md) for complete daemon management reference.
+
+```bash
+# List all running daemons
+bd daemons list --json
+
+# Check health (version mismatches, stale sockets)
+bd daemons health --json
+
+# Stop/restart specific daemon
+bd daemons stop /path/to/workspace --json
+bd daemons restart 12345 --json  # By PID
+
+# View daemon logs
+bd daemons logs /path/to/workspace -n 100
+bd daemons logs 12345 -f  # Follow mode
+
+# Stop all daemons
+bd daemons killall --json
+bd daemons killall --force --json  # Force kill if graceful fails
+```
+
+### Sync Operations
+
+```bash
+# Manual sync (force immediate export/import/commit/push)
+bd sync
+
+# What it does:
+# 1. Export pending changes to JSONL
+# 2. Commit to git
+# 3. Pull from remote
+# 4. Import any updates
+# 5. Push to remote
+```
+
+## Issue Types
+
+- `bug` - Something broken that needs fixing
+- `feature` - New functionality
+- `task` - Work item (tests, docs, refactoring)
+- `epic` - Large feature composed of multiple issues (supports hierarchical children)
+- `chore` - Maintenance work (dependencies, tooling)
+
+**Hierarchical children:** Epics can have child issues with dotted IDs (e.g., `bd-a3f8e9.1`, `bd-a3f8e9.2`). Children are auto-numbered sequentially. Up to 3 levels of nesting supported.
+
+## Priorities
+
+- `0` - Critical (security, data loss, broken builds)
+- `1` - High (major features, important bugs)
+- `2` - Medium (nice-to-have features, minor bugs)
+- `3` - Low (polish, optimization)
+- `4` - Backlog (future ideas)
+
+## Dependency Types
+
+- `blocks` - Hard dependency (issue X blocks issue Y)
+- `related` - Soft relationship (issues are connected)
+- `parent-child` - Epic/subtask relationship
+- `discovered-from` - Track issues discovered during work
+
+Only `blocks` dependencies affect the ready work queue.
+
+**Note:** When creating an issue with a `discovered-from` dependency, the new issue automatically inherits the parent's `source_repo` field.
+
+## Output Formats
+
+### JSON Output (Recommended for Agents)
+
+Always use `--json` flag for programmatic use:
+
+```bash
+# Single issue
+bd show bd-42 --json
+
+# List of issues
+bd ready --json
+
+# Operation result
+bd create "Issue" -p 1 --json
+```
+
+### Human-Readable Output
+
+Default output without `--json`:
+
+```bash
+bd ready
+# bd-42  Fix authentication bug  [P1, bug, in_progress]
+# bd-43  Add user settings page  [P2, feature, open]
+```
+
+## Common Patterns for AI Agents
+
+### Claim and Complete Work
+
+```bash
+# 1. Find available work
+bd ready --json
+
+# 2. Claim issue
+bd update bd-42 --status in_progress --json
+
+# 3. Work on it...
+
+# 4. Close when done
+bd close bd-42 --reason "Implemented and tested" --json
+```
+
+### Discover and Link Work
+
+```bash
+# While working on bd-100, discover a bug
+
+# Old way (two commands):
+bd create "Found auth bug" -t bug -p 1 --json  # Returns bd-101
+bd dep add bd-101 bd-100 --type discovered-from
+
+# New way (one command):
+bd create "Found auth bug" -t bug -p 1 --deps discovered-from:bd-100 --json
+```
+
+### Batch Operations
+
+```bash
+# Update multiple issues at once
+bd update bd-41 bd-42 bd-43 --priority 0 --json
+
+# Close multiple issues
+bd close bd-41 bd-42 bd-43 --reason "Batch completion" --json
+
+# Add label to multiple issues
+bd label add bd-41 bd-42 bd-43 urgent --json
+```
+
+### Session Workflow
+
+```bash
+# Start of session
+bd ready --json  # Find work
+
+# During session
+bd create "..." -p 1 --json
+bd update bd-42 --status in_progress --json
+# ... work ...
+
+# End of session (IMPORTANT!)
+bd sync  # Force immediate sync, bypass debounce
+```
+
+**ALWAYS run `bd sync` at end of agent sessions** to ensure changes are committed/pushed immediately.
+
+## See Also
+
+- [AGENTS.md](../AGENTS.md) - Main agent workflow guide
+- [DAEMON.md](DAEMON.md) - Daemon management and event-driven mode
+- [GIT_INTEGRATION.md](GIT_INTEGRATION.md) - Git workflows and merge strategies
+- [LABELS.md](../LABELS.md) - Label system guide
+- [README.md](../README.md) - User documentation