Add agent-first 'bd onboard' command (bd-173)

- Refactor bd onboard to output instructions instead of doing string replacement
- Leverage agent intelligence to naturally integrate bd into documentation
- Bootstrap via 'BEFORE ANYTHING ELSE: run bd onboard' in AGENTS.md
- Agent receives formatted instructions to update AGENTS.md and CLAUDE.md
- More agentic approach - adapts to existing project structure
- Update README with new bootstrap workflow

Amp-Thread-ID: https://ampcode.com/threads/T-d70fd1bf-8d44-48b6-bb55-5ae49efb23b8
Co-authored-by: Amp <amp@ampcode.com>

AGENTS.md

@@ -447,3 +447,104 @@ See `scripts/README.md` for more details.
 **Remember**: We're building this tool to help AI agents like you! If you find the workflow confusing or have ideas for improvement, create an issue with your feedback.
 
 Happy coding! 🔗
+
+<!-- bd onboard section -->
+## 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"`
+
+### 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!
+
+### 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.
+
+### 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?"
+- ❌ Do NOT create markdown TODO lists
+- ❌ Do NOT use external issue trackers
+- ❌ Do NOT duplicate tracking systems
+
+For more details, see README.md and QUICKSTART.md.
+<!-- /bd onboard section -->