@beads/bd 0.21.5

package/bin/CHANGELOG.md

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+# Changelog
+
+All notable changes to the beads project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.21.4] - 2025-11-02
+
+### Added
+
+- **New Commands**:
+  - `bd status` - Database overview command showing issue counts and stats (bd-28db)
+  - `bd comment` - Convenient alias for `bd comments add` (bd-d3f0)
+  - `bd daemons restart` - Restart specific daemon without manual kill/start
+  - `--json` flag for `bd stale` command
+
+- **Protected Branch Workflow**:
+  - `BEADS_DIR` environment variable for custom database location (bd-e16b)
+  - `sync.branch` configuration for protected branch workflows (bd-b7d2)
+  - Git worktree management with sparse checkout for sync branches (bd-a4b5)
+    - Only checks out `.beads/` in worktrees, minimal disk usage
+    - Only used when `sync.branch` is configured, not for default users
+  - Comprehensive protected branch documentation
+
+- **Migration & Validation**:
+  - Migration inspection tools for AI agents (bd-627d)
+  - Conflict marker detection in `bd import` and `bd validate`
+  - Git hooks health check in `bd doctor`
+  - External reference (`external_ref`) UNIQUE constraint and validation
+  - `external_ref` now primary matching key for import updates (bd-1022)
+
+### Fixed
+
+- **Critical Fixes**:
+  - Daemon corruption from git conflicts (bd-8931)
+  - MCP `set_context` hangs with stdio transport (GH #153)
+  - Double-release race condition in `importInProgress` flag
+  - Critical daemon race condition causing stale exports
+
+- **Configuration & Migration**:
+  - `bd migrate` now detects and sets missing `issue_prefix` config
+  - Config system refactored (renamed `config.json` → `metadata.json`)
+  - Config version update in migrate command
+
+- **Daemon & RPC**:
+  - `bd doctor --json` flag not working (bd-6049)
+  - `bd import` now flushes JSONL immediately for daemon visibility (bd-47f1)
+  - Panic recovery in RPC `handleConnection` (bd-1048)
+  - Daemon auto-upgrades database version instead of exiting
+
+- **Windows Compatibility**:
+  - Windows test failures (path handling, bd binary references)
+  - Windows CI: forward slashes in git hook shell scripts
+  - TestMetricsSnapshot/uptime flakiness on Windows
+
+- **Code Quality**:
+  - All golangci-lint errors fixed - linter now passes cleanly
+  - All gosec, misspell, and unparam linter warnings resolved
+  - Tightened file permissions and added security exclusions
+
+### Changed
+
+- Daemon automatically upgrades database schema version instead of exiting
+- Git worktree management for sync branches uses sparse checkout (`.beads/` only)
+- Improved test isolation and performance optimization
+
+## [0.21.2] - 2025-11-01
+
+### Changed
+- Homebrew formula now auto-published in main repo via GoReleaser
+- Deprecated separate homebrew-beads tap repository
+
+## [0.21.1] - 2025-10-31
+
+### Changed
+- Version bump for consistency across CLI, MCP server, and plugin
+
+## [0.20.1] - 2025-10-31
+
+### Breaking Changes
+
+- **Hash-Based IDs Now Default**: Sequential IDs (bd-1, bd-2) replaced with hash-based IDs (bd-a1b2, bd-f14c)
+  - 4-character hashes for 0-500 issues
+  - 5-character hashes for 500-1,500 issues  
+  - 6-character hashes for 1,500-10,000 issues
+  - Progressive length extension prevents collisions with birthday paradox math
+  - **Migration required**: Run `bd migrate` to upgrade schema (removes `issue_counters` table)
+  - Existing databases continue working - migration is opt-in
+  - Dramatically reduces merge conflicts in multi-worker/multi-branch workflows
+  - Eliminates ID collision issues when multiple agents create issues concurrently
+
+### Removed
+
+- **Sequential ID Generation**: Removed `SyncAllCounters()`, `AllocateNextID()`, and collision remapping logic (bd-c7af, bd-8e05, bd-4c74)
+  - Hash IDs handle collisions by extending hash length, not remapping
+  - `issue_counters` table removed from schema
+  - `--resolve-collisions` flag removed from import (no longer needed)
+  - 400+ lines of obsolete collision handling code removed
+
+### Changed
+
+- **Collision Handling**: Automatic hash extension on collision instead of ID remapping
+  - Much simpler and more reliable than sequential remapping
+  - No cross-branch coordination needed
+  - Birthday paradox ensures extremely low collision rates
+
+### Migration Notes
+
+**For users upgrading from 0.20.0 or earlier:**
+
+1. Run `bd migrate` to detect and upgrade old database schemas
+2. Database continues to work without migration, but you'll see warnings
+3. Hash IDs provide better multi-worker reliability at the cost of non-numeric IDs
+4. Old sequential IDs like `bd-152` become hash IDs like `bd-f14c`
+
+See README.md for hash ID format details and birthday paradox collision analysis.
+
+## [0.20.0] - 2025-10-30
+
+### Added
+- **Hash-Based IDs**: New collision-resistant ID system (bd-168, bd-166, bd-167)
+  - 6-character hash IDs with progressive 7/8-char fallback on collision
+  - Opt-in via `.beads/config.toml` with `id_mode = "hash"`
+  - Migration tool: `bd migrate --to-hash-ids` for existing databases
+  - Prefix-optional ID parsing (e.g., `bd-abc123` or just `abc123`)
+  - Hierarchical child ID generation for discovered-from relationships
+- **Substring ID Matching**: All bd commands now support partial ID matching (bd-170)
+  - `bd show abc` matches any ID containing "abc" (e.g., `bd-abc123`)
+  - Ambiguous matches show helpful error with all candidates
+- **Daemon Registry**: Multi-daemon management for multiple workspaces (bd-07b8c8)
+  - `bd daemons list` shows all running daemons across workspaces
+  - `bd daemons health` detects version mismatches and stale sockets
+  - `bd daemons logs <workspace>` for per-daemon log viewing
+  - `bd daemons killall` to restart all daemons after upgrades
+
+### Fixed
+- **Test Stability**: Deprecated sequence-ID collision tests
+  - Kept `TestFiveCloneCollision` for hash-ID multi-clone testing
+  - Fixed `TestTwoCloneCollision` to use merge instead of rebase
+- **Linting**: golangci-lint v2.5.0 compatibility
+  - Added `version: 2` field to `.golangci.yml`
+  - Renamed `exclude` to `exclude-patterns` for v3 format
+
+### Changed
+- **Multiple bd Detection**: Warning when multiple bd binaries in PATH (PR #182)
+  - Prevents confusion from version conflicts
+  - Shows locations of all bd binaries found
+
+## [0.17.7] - 2025-10-26
+
+### Fixed
+- **Test Isolation**: Export test failures due to hash caching between subtests
+  - Added `ClearAllExportHashes()` method to SQLiteStorage for test isolation
+  - Export tests now properly reset state between subtests
+  - Fixes intermittent test failures when running full test suite
+
+## [0.17.2] - 2025-10-25
+
+### Added
+- **Configurable Sort Policy**: `bd ready --sort` flag for work queue ordering (bd-147)
+  - `hybrid` (default): Priority-weighted by staleness
+  - `priority`: Strict priority ordering for autonomous systems
+  - `oldest`: Pure FIFO for long-tail work
+- **Release Automation**: New scripts for streamlined releases
+  - `scripts/release.sh`: Full automated release (version bump, tests, tag, Homebrew, install)
+  - `scripts/update-homebrew.sh`: Automated Homebrew formula updates
+
+### Fixed
+- **Critical**: Database reinitialization test re-landed with CI fixes (bd-130)
+  - Windows: Fixed git path handling (forward slash normalization)
+  - Nix: Skip test when git unavailable
+  - JSON: Increased scanner buffer to 64MB for large issues
+- **Bug**: Stale daemon socket detection (bd-137)
+  - MCP server now health-checks cached connections before use
+  - Auto-reconnect with exponential backoff on stale sockets
+  - Handles daemon restarts/upgrades gracefully
+- **Linting**: Fixed all errcheck warnings in production code (bd-58)
+  - Proper error handling for database resources and transactions
+  - Graceful EOF handling in interactive input
+- **Linting**: Fixed revive style issues (bd-56)
+  - Removed unused parameters, renamed builtin shadowing
+- **Linting**: Fixed goconst warnings (bd-116)
+
+## [0.17.0] - 2025-10-24
+
+### Added
+- **Git Hooks**: Automatic installation prompt during `bd init` (bd-51)
+  - Eliminates race condition between auto-flush and git commits
+  - Pre-commit hook: Flushes pending changes immediately before commit
+  - Post-merge hook: Imports updated JSONL after pull/merge
+  - Optional installation with Y/n prompt (defaults to yes)
+  - See [examples/git-hooks/README.md](examples/git-hooks/README.md) for details
+- **Duplicate Detection**: New `bd duplicates` command for finding and merging duplicate issues (bd-119, bd-203)
+  - Automated duplicate detection with content-based matching
+  - `--auto-merge` flag for batch merging duplicates
+  - `--dry-run` mode to preview merges before execution
+  - Helps maintain database cleanliness after imports
+- **External Reference Import**: Smart import matching using `external_ref` field (bd-66-74, GH #142)
+  - Issues with `external_ref` match by reference first, not content
+  - Enables hybrid workflows with Jira, GitHub, Linear
+  - Updates existing issues instead of creating duplicates
+  - Database index on `external_ref` for fast lookups
+- **Multi-Database Warning**: Detect and warn about nested beads databases (bd-75)
+  - Prevents accidental creation of multiple databases in hierarchy
+  - Helps users avoid confusion about which database is active
+
+### Fixed
+- **Critical**: Database reinitialization data loss bug (bd-130, DATABASE_REINIT_BUG.md)
+  - Fixed bug where removing `.beads/` and running `bd init` would lose git-tracked issues
+  - Now correctly imports from JSONL during initialization
+  - Added comprehensive tests (later reverted due to CI issues on Windows/Nix)
+- **Critical**: Foreign key constraint regression (bd-62, GH #144)
+  - Pinned modernc.org/sqlite to v1.38.2 to avoid FK violations
+  - Prevents database corruption from upstream regression
+- **Critical**: Install script safety (GH #143 by @marcodelpin)
+  - Prevents shell corruption from directory deletion during install
+  - Restored proper error codes for safer installation
+- **Bug**: Daemon auto-start reliability (bd-137)
+  - Daemon now responsive immediately, runs initial sync in background
+  - Fixes timeout issues when git pull is slow
+  - Skip daemon-running check for forked child process
+- **Bug**: Dependency timestamp churn during auto-import (bd-45, bd-137)
+  - Auto-import no longer updates timestamps on unchanged dependencies
+  - Eliminates perpetually dirty JSONL from metadata changes
+- **Bug**: Import reporting accuracy (bd-49, bd-88)
+  - `bd import` now correctly reports "X updated, Y unchanged" instead of "0 updated"
+  - Better visibility into import operation results
+- **Bug**: Memory database handling
+  - Fixed :memory: database connection with shared cache mode
+  - Proper URL construction for in-memory testing
+
+### Changed
+- **Removed**: Deprecated `bd repos` command
+  - Global daemon architecture removed in favor of per-project daemons
+  - Eliminated cross-project database confusion
+- **Documentation**: Major reorganization and improvements
+  - Condensed README, created specialized docs (QUICKSTART.md, ADVANCED.md, etc.)
+  - Enhanced "Why not GitHub Issues?" FAQ section
+  - Added Beadster to Community & Ecosystem section
+
+### Performance
+- Test coverage improvements: 46.0% → 57.7% (+11.7%)
+  - Added tests for RPC, storage, cmd/bd helpers
+  - New test files: coverage_test.go, helpers_test.go, epics_test.go
+
+### Community
+- Community contribution by @marcodelpin (install script safety fixes)
+- Dependabot integration for automated dependency updates
+
+## [0.16.0] - 2025-10-23
+
+### Added
+- **Automated Releases**: GoReleaser workflow for cross-platform binaries (bd-46)
+  - Automatic GitHub releases on version tags
+  - Linux, macOS, Windows binaries for amd64 and arm64
+  - Checksums and changelog generation included
+- **PyPI Automation**: Automated MCP server publishing to PyPI
+  - GitHub Actions workflow publishes beads-mcp on version tags
+  - Eliminates manual PyPI upload step
+- **Sandbox Mode**: `--sandbox` flag for Claude Code integration (bd-35)
+  - Isolated environment for AI agent experimentation
+  - Prevents production database modifications during testing
+
+### Fixed
+- **Critical**: Idempotent import timestamp churn (bd-84)
+  - Prevents timestamp updates when issue content unchanged
+  - Reduces JSONL churn and git noise from repeated imports
+- **Bug**: Windows CI test failures (bd-60, bd-99)
+  - Fixed path separator issues and file handling on Windows
+  - Skipped flaky tests to stabilize CI
+
+### Changed
+- **Configuration Migration**: Unified config management with Viper (bd-40-44, bd-78)
+  - Migrated from manual env var handling to Viper
+  - Bound all global flags to Viper for consistency
+  - Kept `bd config` independent from Viper for modularity
+  - Added comprehensive configuration tests
+- **Documentation Refactor**: Improved documentation structure
+  - Condensed main README
+  - Created specialized guides (QUICKSTART.md, CONFIG.md, etc.)
+  - Enhanced FAQ and community sections
+
+### Testing
+- Hardened `issueDataChanged` with type-safe comparisons
+- Improved test isolation and reliability
+
+## [0.15.0] - 2025-10-23
+
+### Added
+- **Configuration System**: New `bd config` command for managing configuration (GH #115)
+  - Environment variable definitions with validation
+  - Configuration file support (TOML/YAML/JSON)
+  - Get/set/list/unset commands for user-friendly management
+  - Validation and type checking for config values
+  - Documentation in CONFIG.md
+
+### Fixed
+- **MCP Server**: Smart routing for lifecycle status changes in `update` tool (GH #123)
+  - `update(status="closed")` now routes to `close()` tool to respect approval workflows
+  - `update(status="open")` now routes to `reopen()` tool to respect approval workflows
+  - Prevents bypass of Claude Code approval settings for lifecycle events
+  - bd CLI remains unopinionated; routing happens only in MCP layer
+  - Users can now safely auto-approve benign updates (priority, notes) without exposing closure bypass
+
+## [0.14.0] - 2025-10-22
+
+### Added
+- **Lifecycle Safety Documentation**: Complete documentation for UnderlyingDB() usage (bd-64)
+  - Added tracking guidelines for database lifecycle safety
+  - Documented transaction management best practices
+  - Prevents UAF (use-after-free) bugs in extensions
+
+### Fixed
+- **Critical**: Git worktree detection and warnings (bd-73)
+  - Added automatic detection when running in git worktrees
+  - Displays prominent warning if daemon mode is active in worktree
+  - Prevents daemon from committing/pushing to wrong branch
+  - Documents `--no-daemon` flag as solution for worktree users
+- **Critical**: Multiple daemon race condition (bd-54)
+  - Implemented file locking (`daemon.lock`) to prevent multiple daemons per repository
+  - Uses `flock` on Unix, `LockFileEx` on Windows for process-level exclusivity
+  - Lock held for daemon lifetime, automatically released on exit
+  - Eliminates race conditions in concurrent daemon start attempts
+  - Backward compatible: Falls back to PID check for pre-lock daemons during upgrades
+- **Bug**: daemon.lock tracked in git
+  - Removed daemon.lock from git tracking
+  - Added to .gitignore to prevent future commits
+- **Bug**: Regression in Nix Flake (#110)
+  - Fixed flake build issues
+  - Restored working Nix development environment
+
+### Changed
+- UnderlyingDB() deprecated for most use cases
+  - New UnderlyingConn(ctx) provides safer scoped access
+  - Reduced risk of UAF bugs in database extensions
+  - Updated EXTENDING.md with migration guide
+
+### Documentation
+- Complete release process documentation in RELEASING.md
+- Enhanced EXTENDING.md with lifecycle safety patterns
+- Added UnderlyingDB() tracking guidelines
+
+## [0.11.0] - 2025-10-22
+
+### Added
+- **Issue Merging**: New `bd merge` command for consolidating duplicate issues (bd-7, bd-11-17)
+  - Merge multiple source issues into a single target issue
+  - Automatically migrates all dependencies and dependents to target
+  - Updates text references (bd-X mentions) across all issue fields
+  - Closes source issues with "Merged into bd-Y" reason
+  - Supports `--dry-run` for validation without changes
+  - Example: `bd merge bd-42 bd-43 --into bd-41`
+- **Multi-ID Operations**: Batch operations for increased efficiency (bd-195, #101)
+  - `bd update`: Update multiple issues at once
+  - `bd show`: View multiple issues in single call
+  - `bd label add/remove`: Apply labels to multiple issues
+  - `bd close`: Close multiple issues with one command
+  - `bd reopen`: Reopen multiple issues together
+  - Example: `bd close bd-1 bd-2 bd-3 --reason "Done"`
+- **Daemon RPC Improvements**: Enhanced sync operations (bd-2)
+  - `bd sync` now works correctly in daemon mode
+  - Export operations properly supported via RPC
+  - Prevents database access conflicts during sync
+- **Acceptance Criteria Alias**: Added `--acceptance-criteria` flag (bd-228, #102)
+  - Backward-compatible alias for `--acceptance` in `bd update`
+  - Improves clarity and matches field name
+
+### Fixed
+- **Critical**: Test isolation and database pollution (bd-1, bd-15, bd-19, bd-52)
+  - Comprehensive test isolation ensuring tests never pollute production database
+  - Fixed stress test issues writing 1000+ test issues to production
+  - Quarantined RPC benchmarks to prevent pollution
+  - Added database isolation canary tests
+- **Critical**: Daemon cache staleness (bd-49)
+  - Daemon now detects external database modifications via mtime check
+  - Prevents serving stale data after external `bd import`, `rm bd.db`, etc.
+  - Cache automatically invalidates when DB file changes
+- **Critical**: Counter desync after deletions (bd-49)
+  - Issue counters now sync correctly after bulk deletions
+  - Prevents ID gaps and counter drift
+- **Critical**: Labels and dependencies not persisted in daemon mode (#101)
+  - Fixed label operations failing silently in daemon mode
+  - Fixed dependency operations not saving in daemon mode
+  - Both now correctly propagate through RPC layer
+- **Daemon sync support**: `bd sync` command now works in daemon mode (bd-2)
+  - Previously crashed with nil pointer when daemon running
+  - Export operations now properly routed through RPC
+- **Acceptance flag normalization**: Unified `--acceptance` flag behavior (bd-228, #102)
+  - Added `--acceptance-criteria` as clearer alias
+  - Both flags work identically for backward compatibility
+- **Auto-import Git conflicts**: Better detection of merge conflicts (bd-270)
+  - Auto-import detects and warns about unresolved Git merge conflicts
+  - Prevents importing corrupted JSONL with conflict markers
+  - Clear instructions for resolving conflicts
+
+### Changed
+- **BREAKING**: Removed global daemon socket fallback (bd-231)
+  - Each project now must use its own local daemon (.beads/bd.sock)
+  - Prevents cross-project daemon connections and database pollution
+  - Migration: Stop any global daemon and restart with `bd daemon` in each project
+  - Warning displayed if old global socket (~/.beads/bd.sock) is found
+- **Database cleanup**: Project database cleaned from 1000+ to 55 issues
+  - Removed accumulated test pollution from stress testing
+  - Renumbered issues for clean ID space (bd-1 through bd-55)
+  - Better test isolation prevents future pollution
+
+### Deprecated
+- Global daemon socket support (see BREAKING change above)
+
+## [0.10.0] - 2025-10-20
+
+### Added
+- **Agent Onboarding**: New `bd onboard` command for agent-first documentation (bd-173)
+  - Outputs structured instructions for agents to integrate bd into documentation
+  - Bootstrap workflow: Add 'BEFORE ANYTHING ELSE: run bd onboard' to AGENTS.md
+  - Agent adapts instructions to existing project structure
+  - More agentic approach vs. direct string replacement
+  - Updates README with new bootstrap workflow
+
+## [0.9.11] - 2025-10-20
+
+### Added
+- **Labels Documentation**: Comprehensive LABELS.md guide (bd-159, bd-163)
+  - Complete label system documentation with workflows and best practices
+  - Common label patterns (components, domains, size, quality gates, releases)
+  - Advanced filtering techniques and integration examples
+  - Added Labels section to README with quick reference
+
+### Fixed
+- **Critical**: MCP server crashes on None/null responses (bd-172, fixes #79)
+  - Added null safety checks in `list_issues()`, `ready()`, and `stats()` methods
+  - Returns empty arrays/dicts instead of crashing on None responses
+  - Prevents TypeError when daemon returns empty results
+
+## [0.9.10] - 2025-10-18
+
+### Added
+- **Label Filtering**: Enhanced `bd list` command with label-based filtering (bd-161)
+  - `--label` (or `-l`): Filter by multiple labels with AND semantics (must have ALL)
+  - `--label-any`: Filter by multiple labels with OR semantics (must have AT LEAST ONE)
+  - Examples:
+    - `bd list --label backend,urgent`: Issues with both 'backend' AND 'urgent'
+    - `bd list --label-any frontend,backend`: Issues with either 'frontend' OR 'backend'
+  - Works in both daemon and direct modes
+  - Includes comprehensive test coverage
+- **Log Rotation**: Automatic daemon log rotation with configurable limits (bd-154)
+  - Prevents unbounded log file growth for long-running daemons
+  - Configurable via environment variables: `BEADS_DAEMON_LOG_MAX_SIZE`, `BEADS_DAEMON_LOG_MAX_BACKUPS`, `BEADS_DAEMON_LOG_MAX_AGE`
+  - Optional compression of rotated logs
+  - Defaults: 10MB max size, 3 backups, 7 day retention, compression enabled
+- **Batch Deletion**: Enhanced `bd delete` command with batch operations (bd-127)
+  - Delete multiple issues at once: `bd delete bd-1 bd-2 bd-3 --force`
+  - Read from file: `bd delete --from-file deletions.txt --force`
+  - Dry-run mode: `--dry-run` to preview deletions before execution
+  - Cascade mode: `--cascade` to recursively delete all dependents
+  - Force mode: `--force` to orphan dependents instead of failing
+  - Atomic transactions: all deletions succeed or none do
+  - Comprehensive statistics: tracks deleted issues, dependencies, labels, and events
+
+### Fixed
+- **Critical**: `bd list --status all` showing 0 issues (bd-148)
+  - Status filter now treats "all" as special value meaning "show all statuses"
+  - Previously treated "all" as literal status value, matching no issues
+
+## [0.9.9] - 2025-10-17
+
+### Added
+- **Daemon RPC Architecture**: Production-ready RPC protocol for client-daemon communication (bd-110, bd-111, bd-112, bd-114, bd-117)
+  - Unix socket-based RPC enables faster command execution via long-lived daemon process
+  - Automatic client detection with graceful fallback to direct mode
+  - Serializes SQLite writes and batches git operations to prevent concurrent access issues
+  - Resolves database corruption, git lock contention, and ID counter conflicts with multiple agents
+  - Comprehensive integration tests and stress testing with 4+ concurrent agents
+- **Issue Deletion**: `bd delete` command for removing issues with comprehensive cleanup
+  - Safely removes issues from database and JSONL export
+  - Cleans up dependencies and references to deleted issues
+  - Works correctly with git-based workflows
+- **Issue Restoration**: `bd restore` command for recovering compacted/deleted issues
+  - Restores issues from git history when needed
+  - Preserves references and dependency relationships
+- **Prefix Renaming**: `bd rename-prefix` command for batch ID prefix changes
+  - Updates all issue IDs and text references throughout the database
+  - Useful for project rebranding or namespace changes
+- **Comprehensive Testing**: Added scripttest-based integration tests (#59)
+  - End-to-end coverage for CLI workflows
+  - Tests for init command edge cases (bd-70)
+
+### Fixed
+- **Critical**: Metadata errors causing crashes on first import (bd-663)
+  - Auto-import now treats missing metadata as first import instead of failing
+  - Eliminates initialization errors in fresh repositories
+- **Critical**: N+1 query pattern in auto-import (bd-666)
+  - Replaced per-issue queries with batch fetching
+  - Dramatically improves performance for large imports
+- **Critical**: Duplicate issue imports (bd-421)
+  - Added deduplication logic to prevent importing same issue multiple times
+  - Maintains data integrity during repeated imports
+- **Bug**: Auto-flush missing after renumber/rename-prefix (bd-346)
+  - Commands now properly export to JSONL after completion
+  - Ensures git sees latest changes immediately
+- **Bug**: Renumber ID collision with UUID temp IDs (bd-345)
+  - Uses proper UUID-based temporary IDs to prevent conflicts during renumbering
+  - ID counter now correctly syncs after renumbering operations
+- **Bug**: Collision resolution dependency handling (bd-437)
+  - Uses unchecked dependency addition during collision remapping
+  - Prevents spurious cycle detection errors
+- **Bug**: macOS crashes documented (closes #3, bd-87)
+  - Added CGO_ENABLED=1 workaround documentation for macOS builds
+
+### Changed
+- CLI commands now prefer RPC when daemon is running
+  - Improved error reporting and diagnostics for RPC failures
+  - More consistent exit codes and status messages
+- Internal command architecture refactored for RPC client/server sharing
+  - Reduced code duplication between direct and daemon modes
+  - Improved reliability of background operations
+- Ready work sort order flipped to show oldest issues first
+  - Helps prioritize long-standing work items
+
+### Performance
+- Faster command execution through RPC-backed daemon (up to 10x improvement)
+- N+1 query elimination in list/show operations
+- Reduced write amplification from improved auto-flush behavior
+- Cycle detection performance benchmarks added (bd-311)
+
+### Testing
+- Integration tests for daemon RPC request/response flows
+- End-to-end coverage for delete/restore lifecycles  
+- Regression tests for metadata handling, auto-flush, ID counter sync
+- Comprehensive tests for collision detection in auto-import (bd-401)
+
+### Documentation
+- Release process documentation added (RELEASING.md)
+- Multiple workstreams warning banner for development coordination
+
+## [0.9.8] - 2025-10-16
+
+### Added
+- **Background Daemon Mode**: `bd daemon` command for continuous auto-sync (#bd-386)
+  - Watches for changes and automatically exports to JSONL
+  - Monitors git repository for incoming changes and auto-imports
+  - Production-ready with graceful shutdown, PID file management, and signal handling
+  - Eliminates manual export/import in active development workflows
+- **Git Synchronization**: `bd sync` command for automated git workflows (#bd-378)
+  - One-command sync: stage, commit, pull, push JSONL changes
+  - Automatic merge conflict resolution with collision remapping
+  - Status reporting shows sync progress and any issues
+  - Ideal for distributed teams and CI/CD integration
+- **Issue Compaction**: `bd compact` command to summarize old closed issues (bd-254-264)
+  - AI-powered summarization using Claude Haiku
+  - Reduces database size while preserving essential information
+  - Configurable thresholds for age, dependencies, and references
+  - Compaction status visible in `bd show` output
+- **Label and Title Filtering**: Enhanced `bd list` command (#45, bd-269)
+  - Filter by labels: `bd list --label bug,critical`
+  - Filter by title: `bd list --title "auth"`
+  - Combine with status/priority filters
+- **List Output Formats**: `bd list --format` flag for custom output (PR #46)
+  - Format options: `default`, `compact`, `detailed`, `json`
+  - Better integration with scripts and automation tools
+- **MCP Reopen Support**: Reopen closed issues via MCP server
+  - Claude Desktop plugin can now reopen issues
+  - Useful for revisiting completed work
+- **Cross-Type Cycle Prevention**: Dependency cycles detected across all types (bd-312)
+  - Prevents A→B→A cycles even when mixing `blocks`, `related`, etc.
+  - Semantic validation for parent-child direction
+  - Diagnostic warnings when cycles detected
+
+### Fixed
+- **Critical**: Auto-import collision skipping bug (bd-393, bd-228)
+  - Import would silently skip collisions instead of remapping
+  - Could cause data loss when merging branches
+  - Now correctly applies collision resolution with remapping
+- **Critical**: Transaction state corruption (bd-221)
+  - Nested transactions could corrupt database state
+  - Fixed with proper transaction boundary handling
+- **Critical**: Concurrent temp file collisions (bd-306, bd-373)
+  - Multiple `bd` processes would collide on shared `.tmp` filename
+  - Now uses PID suffix for temp files: `.beads/issues.jsonl.tmp.12345`
+- **Critical**: Circular dependency detection gaps (bd-307)
+  - Some cycle patterns were missed by detection algorithm
+  - Enhanced with comprehensive cycle prevention
+- **Bug**: False positive merge conflict detection (bd-313, bd-270)
+  - Auto-import would detect conflicts when none existed
+  - Fixed with improved Git conflict marker detection
+- **Bug**: Import timeout with large issue sets (bd-199)
+  - 200+ issue imports would timeout
+  - Optimized import performance
+- **Bug**: Collision resolver missing ID counter sync (bd-331)
+  - After remapping, ID counters weren't updated
+  - Could cause duplicate IDs in subsequent creates
+- **Bug**: NULL handling in statistics for empty databases (PR #37)
+  - `bd stats` would crash on newly initialized databases
+  - Fixed NULL value handling in GetStatistics
+
+### Changed
+- Compaction removes snapshot/restore (simplified to permanent decay)
+- Export file writing refactored to avoid Windows Defender false positives (PR #31)
+- Error handling improved in auto-import and fallback paths (PR #47)
+- Reduced cyclomatic complexity in main.go (PR #48)
+- MCP integration tests fixed and linting cleaned up (PR #40)
+
+### Performance
+- Cycle detection benchmarks added (bd-311)
+- Import optimization for large issue sets
+- Export uses PID-based temp files to avoid lock contention
+
+### Community
+- Merged PR #31: Windows Defender mitigation for export
+- Merged PR #37: Fix NULL handling in statistics
+- Merged PR #38: Nix flake for declarative builds
+- Merged PR #40: MCP integration test fixes
+- Merged PR #45: Label and title filtering for bd list
+- Merged PR #46: Add --format flag to bd list
+- Merged PR #47: Error handling consistency
+- Merged PR #48: Cyclomatic complexity reduction
+
+## [0.9.2] - 2025-10-14
+
+### Added
+- **One-Command Dependency Creation**: `--deps` flag for `bd create` (#18)
+  - Create issues with dependencies in a single command
+  - Format: `--deps type:id` or just `--deps id` (defaults to blocks)
+  - Multiple dependencies: `--deps discovered-from:bd-20,blocks:bd-15`
+  - Whitespace-tolerant parsing
+  - Particularly useful for AI agents creating discovered-from issues
+- **External Reference Tracking**: `external_ref` field for linking to external trackers
+  - Link bd issues to GitHub, Jira, Linear, etc.
+  - Example: `bd create "Issue" --external-ref gh-42`
+  - `bd update` supports updating external references
+  - Tracked in JSONL for git portability
+- **Metadata Storage**: Internal metadata table for system state
+  - Stores import hash for idempotent auto-import
+  - Enables future extensibility for system preferences
+  - Auto-migrates existing databases
+- **Windows Support**: Complete Windows 11 build instructions (#10)
+  - Tested with mingw-w64
+  - Full CGo support documented
+  - PATH setup instructions
+- **Go Extension Example**: Complete working example of database extensions (#15)
+  - Demonstrates custom table creation
+  - Shows cross-layer queries joining with issues
+  - Includes test suite and documentation
+- **Issue Type Display**: `bd list` now shows issue type in output (#17)
+  - Better visibility: `bd-1 [P1] [bug] open`
+  - Helps distinguish bugs from features at a glance
+
+### Fixed
+- **Critical**: Dependency tree deduplication for diamond dependencies (bd-85, #1)
+  - Fixed infinite recursion in complex dependency graphs
+  - Prevents duplicate nodes at same level
+  - Handles multiple blockers correctly
+- **Critical**: Hash-based auto-import replaces mtime comparison (bd-84)
+  - Git pull updates mtime but may not change content
+  - Now uses SHA256 hash to detect actual changes
+  - Prevents unnecessary imports after git operations
+- **Critical**: Parallel issue creation race condition (PR #8, bd-66)
+  - Multiple processes could generate same ID
+  - Replaced in-memory counter with atomic database counter
+  - Syncs counters after import to prevent collisions
+  - Comprehensive test coverage
+
+### Changed
+- Auto-import now uses content hash instead of modification time
+- Dependency tree visualization improved for complex graphs
+- Better error messages for dependency operations
+
+### Community
+- Merged PR #8: Parallel issue creation fix
+- Merged PR #10: Windows build instructions
+- Merged PR #12: Fix quickstart EXTENDING.md link
+- Merged PR #14: Better enable Go extensions
+- Merged PR #15: Complete Go extension example
+- Merged PR #17: Show issue type in list output
+
+## [0.9.1] - 2025-10-14
+
+### Added
+- **Incremental JSONL Export**: Major performance optimization
+  - Dirty issue tracking system to only export changed issues
+  - Auto-flush with 5-second debounce after CRUD operations
+  - Automatic import when JSONL is newer than database
+  - `--no-auto-flush` and `--no-auto-import` flags for manual control
+  - Comprehensive test coverage for auto-flush/import
+- **ID Space Partitioning**: Explicit ID assignment for parallel workers
+  - `bd create --id worker1-100` for controlling ID allocation
+  - Enables multiple agents to work without conflicts
+  - Documented in CLAUDE.md for agent workflows
+- **Auto-Migration System**: Seamless database schema upgrades
+  - Automatically adds dirty_issues table to existing databases
+  - Silent migration on first access after upgrade
+  - No manual intervention required
+
+### Fixed
+- **Critical**: Race condition in dirty tracking (TOCTOU bug)
+  - Could cause data loss during concurrent operations
+  - Fixed by tracking specific exported IDs instead of clearing all
+- **Critical**: Export with filters cleared all dirty issues
+  - Status/priority filters would incorrectly mark non-matching issues as clean
+  - Now only clears issues that were actually exported
+- **Bug**: Malformed ID detection never worked
+  - SQLite CAST returns 0 for invalid strings, not NULL
+  - Now correctly detects non-numeric ID suffixes like "bd-abc"
+  - No false positives on legitimate zero-prefixed IDs
+- **Bug**: Inconsistent dependency dirty marking
+  - Duplicated 20+ lines of code in AddDependency/RemoveDependency
+  - Refactored to use shared markIssuesDirtyTx() helper
+- Fixed unchecked error in import.go when unmarshaling JSON
+- Fixed unchecked error returns in test cleanup code
+- Removed duplicate test code in dependencies_test.go
+- Fixed Go version in go.mod (was incorrectly set to 1.25.2)
+
+### Changed
+- Export now tracks which specific issues were exported
+- ClearDirtyIssuesByID() added (ClearDirtyIssues() deprecated with race warning)
+- Dependency operations use shared dirty-marking helper (DRY)
+
+### Performance
+- Incremental export: Only writes changed issues (vs full export)
+- Regex caching in ID replacement: 1.9x performance improvement
+- Automatic debounced flush prevents excessive I/O
+
+## [0.9.0] - 2025-10-12
+
+### Added
+- **Collision Resolution System**: Automatic ID remapping for import collisions
+  - Reference scoring algorithm to minimize updates during remapping
+  - Word-boundary regex matching to prevent false replacements
+  - Automatic updating of text references and dependencies
+  - `--resolve-collisions` flag for safe branch merging
+  - `--dry-run` flag to preview collision detection
+- **Export/Import with JSONL**: Git-friendly text format
+  - Dependencies embedded in JSONL for complete portability
+  - Idempotent import (exact matches detected)
+  - Collision detection (same ID, different content)
+- **Ready Work Algorithm**: Find issues with no open blockers
+  - `bd ready` command shows unblocked work
+  - `bd blocked` command shows what's waiting
+- **Dependency Management**: Four dependency types
+  - `blocks`: Hard blocker (affects ready work)
+  - `related`: Soft relationship
+  - `parent-child`: Epic/subtask hierarchy
+  - `discovered-from`: Track issues discovered during work
+- **Database Discovery**: Auto-find database in project hierarchy
+  - Walks up directory tree like git
+  - Supports `$BEADS_DB` environment variable
+  - Falls back to `~/.beads/default.db`
+- **Comprehensive Documentation**:
+  - README.md with 900+ lines of examples and FAQs
+  - CLAUDE.md for AI agent integration patterns
+  - SECURITY.md with security policy and best practices
+  - TEXT_FORMATS.md analyzing JSONL approach
+  - EXTENDING.md for database extension patterns
+  - GIT_WORKFLOW.md for git integration
+- **Examples**: Real-world integration patterns
+  - Python agent implementation
+  - Bash agent script
+  - Git hooks for automatic export/import
+  - Branch merge workflow with collision resolution
+  - Claude Desktop MCP integration (coming soon)
+
+### Changed
+- Switched to JSONL as source of truth (from binary SQLite)
+- SQLite database now acts as ephemeral cache
+- Issue IDs generated with numerical max (not alphabetical)
+- Export sorts issues by ID for consistent git diffs
+
+### Security
+- SQL injection protection via allowlisted field names
+- Input validation for all issue fields
+- File path validation for database operations
+- Warnings about not storing secrets in issues
+
+## [0.1.0] - Initial Development
+
+### Added
+- Core issue tracking (create, update, list, show, close)
+- SQLite storage backend
+- Dependency tracking with cycle detection
+- Label support
+- Event audit trail
+- Full-text search
+- Statistics and reporting
+- `bd init` for project initialization
+- `bd quickstart` interactive tutorial
+
+---
+
+## Version History
+
+- **0.9.8** (2025-10-16): Daemon mode, git sync, compaction, critical bug fixes
+- **0.9.2** (2025-10-14): Community PRs, critical bug fixes, and --deps flag
+- **0.9.1** (2025-10-14): Performance optimization and critical bug fixes
+- **0.9.0** (2025-10-12): Pre-release polish and collision resolution
+- **0.1.0**: Initial development version
+
+## Upgrade Guide
+
+### Upgrading to 0.9.8
+
+No breaking changes. All changes are backward compatible:
+- **bd daemon**: New optional background service for auto-sync workflows
+- **bd sync**: New optional git integration command
+- **bd compact**: New optional command for issue summarization (requires Anthropic API key)
+- **--format flag**: Optional new feature for `bd list`
+- **Label/title filters**: Optional new filters for `bd list`
+- **Bug fixes**: All critical fixes are transparent to users
+
+Simply pull the latest version and rebuild:
+```bash
+go install github.com/steveyegge/beads/cmd/bd@latest
+# or
+git pull && go build -o bd ./cmd/bd
+```
+
+**Note**: The `bd compact` command requires an Anthropic API key in `$ANTHROPIC_API_KEY` environment variable. All other features work without any additional setup.
+
+### Upgrading to 0.9.2
+
+No breaking changes. All changes are backward compatible:
+- **--deps flag**: Optional new feature for `bd create`
+- **external_ref**: Optional field, existing issues unaffected
+- **Metadata table**: Auto-migrates on first use
+- **Bug fixes**: All critical fixes are transparent to users
+
+Simply pull the latest version and rebuild:
+```bash
+go install github.com/steveyegge/beads/cmd/bd@latest
+# or
+git pull && go build -o bd ./cmd/bd
+```
+
+### Upgrading to 0.9.1
+
+No breaking changes. All changes are backward compatible:
+- **Auto-migration**: The dirty_issues table is automatically added to existing databases
+- **Auto-flush/import**: Enabled by default, improves workflow (can disable with flags if needed)
+- **ID partitioning**: Optional feature, use `--id` flag only if needed for parallel workers
+
+If you're upgrading from 0.9.0, simply pull the latest version. Your existing database will be automatically migrated on first use.
+
+### Upgrading to 0.9.0
+
+No breaking changes. The JSONL export format is backward compatible.
+
+If you have issues in your database:
+1. Run `bd export -o .beads/issues.jsonl` to create the text file
+2. Commit `.beads/issues.jsonl` to git
+3. Add `.beads/*.db` to `.gitignore`
+
+New collaborators can clone the repo and run:
+```bash
+bd import -i .beads/issues.jsonl
+```
+
+The SQLite database will be automatically populated from the JSONL file.
+
+## Future Releases
+
+See open issues tagged with milestone markers for planned features in upcoming releases.
+
+For version 1.0, see: `bd dep tree bd-8` (the 1.0 milestone epic)