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fix(autoimport): auto-correct deleted status to tombstone for JSONL compatibility (#1231)

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* fix(autoimport): auto-correct deleted status to tombstone for JSONL compatibility (GH#1223)

This fix addresses the 'Stuck in sync diversion loop' issue where v0.48.0
encountered validation errors during JSONL import. The issue occurs when
JSONL files from older versions have issues with status='deleted' but the
current code expects status='tombstone' for deleted issues.

Changes:
- Add migration logic in parseJSONL to auto-correct 'deleted' status to 'tombstone'
- Ensure tombstones always have deleted_at timestamp set
- Add debug logging for both migration operations
- Prevents users from being stuck in sync divergence when upgrading

Fixes GH#1223: Stuck in sync diversion loop

* fix(autoimport): comprehensively fix corrupted deleted_at on non-tombstone issues (GH#1223)

The initial fix for GH#1223 only caught issues with status='deleted', but the real
data in the wild had issues with status='closed' (or other statuses) but also
had deleted_at set, which violates the validation rule.

Changes:
- Add broader migration logic: any non-tombstone issue with deleted_at should become tombstone
- Apply fix in all three JSONL parsing locations:
  - internal/autoimport/autoimport.go (parseJSONL for auto-import)
  - cmd/bd/import.go (import command)
  - cmd/bd/daemon_sync.go (daemon sync helper)
- Add comprehensive test case for corrupted closed issues with deleted_at
- Fixes the 'non-tombstone issues cannot have deleted_at timestamp' validation error
  during fresh bd init or import

Fixes GH#1223: Stuck in sync diversion loop

* Add merge driver comment to .gitattributes

* fix: properly clean up .gitattributes during bd admin reset

Fixes GH#1223 - Stuck in sync diversion loop

The removeGitattributesEntry() function was not properly cleaning up
beads-related entries from .gitattributes. It only removed lines
containing "merge=beads" but left behind:
- The comment line "# Use bd merge for beads JSONL files"
- Empty lines following removed entries

This caused .gitattributes to remain in a modified state after
bd admin reset --force, triggering sync divergence warning loop.

The fix now:
- Skips lines containing "merge=beads" (existing behavior)
- Skips beads-related comment lines
- Skips empty lines that follow removed beads entries
- Properly cleans up file so it's either empty (and gets deleted)
  or contains only non-beads content

---------

Co-authored-by: Amp <amp@example.com>
This commit is contained in:
matt wilkie
2026-01-21 22:50:38 -07:00
committed by GitHub
parent 1d3ca43620
commit 1f8a6bf84e
13 changed files with 206 additions and 8908 deletions
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<!-- Auto-generated by bd v0.24.2 - DO NOT EDIT MANUALLY -->
<!-- Run 'bd onboard --output .beads/BD_GUIDE.md' to regenerate -->
# BD (Beads) Guide for AI Agents
This file contains canonical bd (beads) workflow instructions for AI agents.
It is auto-generated and version-stamped to track bd upgrades.
> **For project-specific instructions**, see AGENTS.md in the repository root.
> This file only covers bd tool usage, not project-specific workflows.
---
## Issue Tracking with bd (beads)
**IMPORTANT**: This project uses **bd (beads)** for ALL issue tracking. Do NOT use markdown TODOs, task lists, or other tracking methods.
### Why bd?
- Dependency-aware: Track blockers and relationships between issues
- Git-friendly: Auto-syncs to JSONL for version control
- Agent-optimized: JSON output, ready work detection, discovered-from links
- Prevents duplicate tracking systems and confusion
### Quick Start
**Check for ready work:**
```bash
bd ready --json
```
**Create new issues:**
```bash
bd create "Issue title" -t bug|feature|task -p 0-4 --json
bd create "Issue title" -p 1 --deps discovered-from:bd-123 --json
```
**Claim and update:**
```bash
bd update bd-42 --status in_progress --json
bd update bd-42 --priority 1 --json
```
**Complete work:**
```bash
bd close bd-42 --reason "Completed" --json
```
### Issue Types
- `bug` - Something broken
- `feature` - New functionality
- `task` - Work item (tests, docs, refactoring)
- `epic` - Large feature with subtasks
- `chore` - Maintenance (dependencies, tooling)
### Priorities
- `0` - Critical (security, data loss, broken builds)
- `1` - High (major features, important bugs)
- `2` - Medium (default, nice-to-have)
- `3` - Low (polish, optimization)
- `4` - Backlog (future ideas)
### Workflow for AI Agents
1. **Check ready work**: `bd ready` shows unblocked issues
2. **Claim your task**: `bd update <id> --status in_progress`
3. **Work on it**: Implement, test, document
4. **Discover new work?** Create linked issue:
- `bd create "Found bug" -p 1 --deps discovered-from:<parent-id>`
5. **Complete**: `bd close <id> --reason "Done"`
6. **Commit together**: Always commit the `.beads/issues.jsonl` file together with the code changes so issue state stays in sync with code state
### Auto-Sync
bd automatically syncs with git:
- Exports to `.beads/issues.jsonl` after changes (5s debounce)
- Imports from JSONL when newer (e.g., after `git pull`)
- No manual export/import needed!
### GitHub Copilot Integration
If using GitHub Copilot, also create `.github/copilot-instructions.md` for automatic instruction loading.
Run `bd onboard` to get the content, or see step 2 of the onboard instructions.
### MCP Server (Recommended)
If using Claude or MCP-compatible clients, install the beads MCP server:
```bash
pip install beads-mcp
```
Add to MCP config (e.g., `~/.config/claude/config.json`):
```json
{
"beads": {
"command": "beads-mcp",
"args": []
}
}
```
Then use `mcp__beads__*` functions instead of CLI commands.
### Managing AI-Generated Planning Documents
AI assistants often create planning and design documents during development:
- PLAN.md, IMPLEMENTATION.md, ARCHITECTURE.md
- DESIGN.md, CODEBASE_SUMMARY.md, INTEGRATION_PLAN.md
- TESTING_GUIDE.md, TECHNICAL_DESIGN.md, and similar files
**Best Practice: Use a dedicated directory for these ephemeral files**
**Recommended approach:**
- Create a `history/` directory in the project root
- Store ALL AI-generated planning/design docs in `history/`
- Keep the repository root clean and focused on permanent project files
- Only access `history/` when explicitly asked to review past planning
**Example .gitignore entry (optional):**
```
# AI planning documents (ephemeral)
history/
```
**Benefits:**
- ✅ Clean repository root
- ✅ Clear separation between ephemeral and permanent documentation
- ✅ Easy to exclude from version control if desired
- ✅ Preserves planning history for archeological research
- ✅ Reduces noise when browsing the project
### Important Rules
- ✅ Use bd for ALL task tracking
- ✅ Always use `--json` flag for programmatic use
- ✅ Link discovered work with `discovered-from` dependencies
- ✅ Check `bd ready` before asking "what should I work on?"
- ✅ Store AI planning docs in `history/` directory
- ❌ Do NOT create markdown TODO lists
- ❌ Do NOT use external issue trackers
- ❌ Do NOT duplicate tracking systems
- ❌ Do NOT clutter repo root with planning documents
For more details, see README.md and QUICKSTART.md.
---
# GitHub Copilot Instructions for Beads
## Project Overview
**beads** (command: `bd`) is a Git-backed issue tracker designed for AI-supervised coding workflows. We dogfood our own tool for all task tracking.
**Key Features:**
- Dependency-aware issue tracking
- Auto-sync with Git via JSONL
- AI-optimized CLI with JSON output
- Built-in daemon for background operations
- MCP server integration for Claude and other AI assistants
## Tech Stack
- **Language**: Go 1.21+
- **Storage**: SQLite (internal/storage/sqlite/)
- **CLI Framework**: Cobra
- **Testing**: Go standard testing + table-driven tests
- **CI/CD**: GitHub Actions
- **MCP Server**: Python (integrations/beads-mcp/)
## Coding Guidelines
### Testing
- Always write tests for new features
- Use `BEADS_DB=/tmp/test.db` to avoid polluting production database
- Run `go test -short ./...` before committing
- Never create test issues in production DB (use temporary DB)
### Code Style
- Run `golangci-lint run ./...` before committing
- Follow existing patterns in `cmd/bd/` for new commands
- Add `--json` flag to all commands for programmatic use
- Update docs when changing behavior
### Git Workflow
- Always commit `.beads/issues.jsonl` with code changes
- Run `bd sync` at end of work sessions
- Install git hooks: `bd hooks install` (ensures DB ↔ JSONL consistency)
## Issue Tracking with bd
**CRITICAL**: This project uses **bd** for ALL task tracking. Do NOT create markdown TODO lists.
### Essential Commands
```bash
# Find work
bd ready --json # Unblocked issues
bd stale --days 30 --json # Forgotten issues
# Create and manage
bd create "Title" -t bug|feature|task -p 0-4 --json
bd update <id> --status in_progress --json
bd close <id> --reason "Done" --json
# Search
bd list --status open --priority 1 --json
bd show <id> --json
# Sync (CRITICAL at end of session!)
bd sync # Force immediate export/commit/push
```
### Workflow
1. **Check ready work**: `bd ready --json`
2. **Claim task**: `bd update <id> --status in_progress`
3. **Work on it**: Implement, test, document
4. **Discover new work?** `bd create "Found bug" -p 1 --deps discovered-from:<parent-id> --json`
5. **Complete**: `bd close <id> --reason "Done" --json`
6. **Sync**: `bd sync` (flushes changes to git immediately)
### Priorities
- `0` - Critical (security, data loss, broken builds)
- `1` - High (major features, important bugs)
- `2` - Medium (default, nice-to-have)
- `3` - Low (polish, optimization)
- `4` - Backlog (future ideas)
## Project Structure
```
beads/
├── cmd/bd/ # CLI commands (add new commands here)
├── internal/
│ ├── types/ # Core data types
│ └── storage/ # Storage layer
│ └── sqlite/ # SQLite implementation
├── integrations/
│ └── beads-mcp/ # MCP server (Python)
├── examples/ # Integration examples
├── docs/ # Documentation
└── .beads/
├── beads.db # SQLite database (DO NOT COMMIT)
└── issues.jsonl # Git-synced issue storage
```
## Available Resources
### MCP Server (Recommended)
Use the beads MCP server for native function calls instead of shell commands:
- Install: `pip install beads-mcp`
- Functions: `mcp__beads__ready()`, `mcp__beads__create()`, etc.
- See `integrations/beads-mcp/README.md`
### Scripts
- `./scripts/bump-version.sh <version> --commit` - Update all version files atomically
- `./scripts/release.sh <version>` - Complete release workflow
- `./scripts/update-homebrew.sh <version>` - Update Homebrew formula
### Key Documentation
- **AGENTS.md** - Comprehensive AI agent guide (detailed workflows, advanced features)
- **AGENT_INSTRUCTIONS.md** - Development procedures, testing, releases
- **README.md** - User-facing documentation
- **docs/CLI_REFERENCE.md** - Complete command reference
## Important Rules
- ✅ Use bd for ALL task tracking
- ✅ Always use `--json` flag for programmatic use
- ✅ Run `bd sync` at end of sessions
- ✅ Test with `BEADS_DB=/tmp/test.db`
- ❌ Do NOT create markdown TODO lists
- ❌ Do NOT create test issues in production DB
- ❌ Do NOT commit `.beads/beads.db` (JSONL only)
---
**For detailed workflows and advanced features, see [AGENTS.md](../AGENTS.md)**
---
**Generated by bd v0.24.2**
To regenerate this file after upgrading bd:
```bash
bd onboard --output .beads/BD_GUIDE.md
```