refactor(dev): restructure Claude commands/skills directories

Correct terminology mismatch: - Rename skills/ to commands/ (these are user-invokable commands) - Create new skills/ for reference materials - Move bd_workflow.md to skills/ (it's reference material) - Add micro-skills and formulas directories - Update default.nix to install both commands and skills Commands → ~/.claude/commands/ (invokable as /command-name) Skills → ~/.claude/commands/skills/ (reference materials) Formulas → ~/.beads/formulas/ (workflow templates) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-01-15 17:16:55 -08:00
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+---
+description: Comprehensive guide for the beads + humanlayer integrated workflow
+---
+
+# Beads Workflow Guide
+
+This document describes the integrated workflow combining **beads** (issue tracking) with **humanlayer-style skills** (deep research, planning, implementation).
+
+## Philosophy
+
+### Two Systems, Complementary Purposes
+
+| System | Purpose | Storage |
+|--------|---------|---------|
+| **Beads** | Track WHAT work exists | `.beads/` (git-synced) |
+| **Thoughts** | Store HOW to do the work | `thoughts/` (local or symlinked) |
+
+### Autonomy Model
+
+| Bead Type | Agent Autonomy | Checkpoint |
+|-----------|----------------|------------|
+| `research` | **Full** - agent closes when satisfied | None |
+| `feature`, `task`, `bug` | **Checkpointed** - pause for validation | Per-plan |
+
+**Key insight**: Research produces artifacts. Implementation produces commits. Commits are the review boundary.
+
+## Directory Structure
+
+```
+project/
+├── .beads/                              # Beads database (git-synced)
+│   ├── beads.db
+│   ├── config.yaml
+│   └── issues.jsonl
+├── thoughts/                            # Artifacts (local or symlink)
+│   ├── beads-{id}/                      # Per-bead artifacts
+│   │   ├── research.md
+│   │   ├── plan.md
+│   │   └── plan-v1.md                   # Iteration history
+│   └── shared/                          # Legacy/non-bead artifacts
+│       ├── research/
+│       └── plans/
+└── home/roles/development/skills/       # Skill definitions
+    ├── beads_research.md
+    ├── beads_plan.md
+    ├── beads_implement.md
+    └── beads_iterate.md
+```
+
+## When to Use What
+
+### Use Beads When:
+- Work spans multiple sessions
+- Work has dependencies or blockers
+- You need to track status across interruptions
+- Multiple related tasks need coordination
+- Context recovery after compaction matters
+
+### Use TodoWrite When:
+- Single-session execution tracking
+- Breaking down work within a session
+- Tracking progress on a single bead
+
+### Use Both Together:
+- Beads track the overall work items
+- TodoWrite tracks progress within a session
+- Example: Bead for "Implement auth", TodoWrite for each file being edited
+
+## Workflow Patterns
+
+### Pattern 1: Research-First Approach
+
+```
+1. Create research bead
+   bd create --title="Research auth patterns" --type=research --priority=1
+
+2. Run research
+   /beads:research {bead-id}
+   → Agent researches, writes to thoughts/beads-{id}/research.md
+   → Agent closes bead when satisfied
+
+3. Create implementation bead
+   bd create --title="Implement auth" --type=feature --priority=1
+
+4. Plan the implementation
+   /beads:plan {bead-id}
+   → Agent reads prior research, creates plan
+   → Plan saved to thoughts/beads-{id}/plan.md
+
+5. Implement
+   /beads:implement {bead-id}
+   → Agent follows plan, pauses for manual verification
+   → You validate, agent closes bead
+```
+
+### Pattern 2: Direct Implementation
+
+For well-understood tasks without research:
+
+```
+1. Create bead
+   bd create --title="Fix login bug" --type=bug --priority=0
+
+2. Plan and implement
+   /beads:plan {bead-id}
+   → Quick planning based on bead description
+
+   /beads:implement {bead-id}
+   → Follow plan, pause at checkpoint
+```
+
+### Pattern 3: Iterative Planning
+
+When requirements evolve:
+
+```
+1. Initial plan
+   /beads:plan {bead-id}
+
+2. Iterate based on feedback
+   /beads:iterate {bead-id} - add error handling phase
+
+3. Iterate again if needed
+   /beads:iterate {bead-id} - split phase 2 into backend/frontend
+
+4. Implement when plan is solid
+   /beads:implement {bead-id}
+```
+
+### Pattern 4: Parallel Work
+
+Using parallel_beads skill for multiple independent tasks:
+
+```
+1. Check what's ready
+   bd ready
+
+2. Select multiple beads
+   /parallel_beads
+   → Select beads to work on
+   → Each gets worktree, PR, review
+
+3. Reconcile after PRs merge
+   /reconcile_beads
+```
+
+## Skills Reference
+
+### /beads:research {bead-id}
+- Conducts comprehensive codebase research
+- Uses parallel sub-agents for efficiency
+- Outputs to `thoughts/beads-{id}/research.md`
+- **Autonomy**: Can close research beads automatically
+
+### /beads:plan {bead-id}
+- Creates detailed implementation plans
+- Interactive process with checkpoints
+- Outputs to `thoughts/beads-{id}/plan.md`
+- Can create dependent implementation beads
+
+### /beads:implement {bead-id}
+- Follows plans from thoughts/
+- Updates plan checkboxes for resumability
+- **Checkpoint**: Pauses after plan completion for manual verification
+- Only closes bead after human confirms
+
+### /beads:iterate {bead-id}
+- Updates existing plans based on feedback
+- Preserves plan structure while making targeted changes
+- Saves iteration history as `plan-v{N}.md`
+
+### /parallel_beads
+- Orchestrates parallel bead processing
+- Creates worktrees, PRs, reviews for multiple beads
+- Good for batching independent work
+
+### /reconcile_beads
+- Closes beads whose PRs have merged
+- Run after merging PRs to keep beads in sync
+
+## Session Protocols
+
+### Starting a Session
+
+```bash
+# Check what's available
+bd ready
+
+# Pick work and start
+bd update {bead-id} --status=in_progress
+```
+
+### Ending a Session
+
+```bash
+# Always run this checklist:
+[ ] git status                    # Check changes
+[ ] git add <files>               # Stage code changes
+[ ] bd sync                       # Sync beads
+[ ] git commit -m "..."           # Commit code
+[ ] git push                      # Push to remote
+```
+
+### Resuming Work
+
+```bash
+# Find in-progress work
+bd list --status=in_progress
+
+# Check bead notes for context
+bd show {bead-id}
+
+# Check for partial plan progress
+cat thoughts/beads-{id}/plan.md | grep "\[x\]"
+```
+
+## Thoughts Directory Patterns
+
+### For Work Repos (via symlink)
+```
+project/thoughts → ~/thoughts/repos/{repo-name}/
+```
+- Syncs via codelayer to work remote
+- Shared across projects on same machine
+
+### For Personal Repos (local)
+```
+project/thoughts/  # Regular directory, not symlink
+```
+- Stays local to project
+- Committed with project or gitignored
+
+### Determining Which Pattern
+```bash
+# Check if thoughts is a symlink
+ls -la thoughts
+
+# If symlink, it points to ~/thoughts/repos/{repo}/
+# If directory, it's local to this project
+```
+
+## Best Practices
+
+### 1. Bead Descriptions Matter
+Write clear descriptions - they're the input for research and planning:
+```bash
+bd create --title="Implement user preferences" --type=feature \
+  --description="Add user preferences storage and UI.
+
+Requirements:
+- Store preferences in SQLite
+- Expose via REST API
+- Add settings page in UI
+
+See related: thoughts/shared/research/preferences-patterns.md"
+```
+
+### 2. Link Artifacts in Beads
+Always update bead notes with artifact locations:
+```bash
+bd update {id} --notes="Research: thoughts/beads-{id}/research.md
+Plan: thoughts/beads-{id}/plan.md"
+```
+
+### 3. Use Dependencies
+Structure work with dependencies:
+```bash
+# Research blocks planning
+bd dep add {plan-bead} {research-bead}
+
+# Planning blocks implementation
+bd dep add {impl-bead} {plan-bead}
+```
+
+### 4. Trust the Checkpoint Model
+- Research beads: Let agent close them
+- Implementation beads: Always validate before closing
+- If in doubt, err on the side of checkpoints
+
+### 5. Keep Plans Updated
+- Check off completed items as you go
+- Update notes with progress
+- This enables seamless resume across sessions
+
+## Troubleshooting
+
+### "What bead should I work on?"
+```bash
+bd ready  # Shows unblocked work
+```
+
+### "Where did the research go?"
+```bash
+ls thoughts/beads-{id}/
+bd show {id}  # Check notes for artifact links
+```
+
+### "Plan doesn't match reality"
+```bash
+/beads:iterate {id}  # Update plan based on findings
+```
+
+### "Session ended mid-implementation"
+```bash
+bd show {id}  # Check notes for progress
+cat thoughts/beads-{id}/plan.md | grep "\[x\]"  # See completed items
+/beads:implement {id}  # Resume - will pick up from last checkpoint
+```
+
+### "Bead is blocked"
+```bash
+bd show {id}  # See what's blocking
+bd blocked    # See all blocked beads
+```
+
+## Migration Notes
+
+### From Pure Humanlayer to Beads+Humanlayer
+
+Old pattern:
+```
+thoughts/shared/research/2025-01-01-topic.md
+thoughts/shared/plans/2025-01-01-feature.md
+```
+
+New pattern:
+```
+thoughts/beads-{id}/research.md
+thoughts/beads-{id}/plan.md
+```
+
+The `shared/` structure still works for non-bead artifacts, but prefer per-bead directories for tracked work.
+
+### Existing Content
+- Keep existing `thoughts/shared/` content
+- New bead-tracked work uses `thoughts/beads-{id}/`
+- Reference old research from bead descriptions when relevant
+
+## Design Decisions
+
+### Phase Tracking: Artifacts vs Statuses
+
+**Current approach**: Skills infer workflow phase from artifact presence:
+- Has `research.md` → research done
+- Has `plan.md` → planning done
+- No artifacts → needs research/planning
+
+**Alternative considered**: Explicit phase statuses (`needs_research`, `needs_plan`, `implementing`, etc.)
+
+**Why artifacts win**:
+1. **Single source of truth** - Status can't drift from reality
+2. **Less state to maintain** - No need to update status when creating artifacts
+3. **Works across repos** - No custom status config needed
+4. **Skills already check artifacts** - Natural fit with existing behavior
+
+**When explicit statuses would help**:
+- Pipeline visualization (e.g., `bd list --status=needs_plan`)
+- Agent self-selection by phase
+- Team coordination dashboards
+
+**Recommendation**: Keep artifact-inference as primary mechanism. If pipeline visibility becomes important, consider adding statuses that skills auto-set when creating artifacts (advisory, not enforced).
+
+### One Bead Per Feature (Default)
+
+**Current approach**: File one bead per logical feature. Skills handle phases internally.
+
+**Alternative considered**: Separate beads for research → planning → implementation, linked by dependencies.
+
+**Why single bead wins for most work**:
+1. **Lower friction** - Quick idea dump without filing 3 tickets
+2. **Simpler tracking** - One status to check
+3. **Natural grouping** - Artifacts stay together in `thoughts/beads-{id}/`
+
+**When to split into multiple beads**:
+- Research reveals the work should be multiple features
+- Different phases need different assignees
+- Explicit dependency tracking matters (e.g., "auth must ship before payments")
+
+**The discovered-work pattern**: Start with one bead. If research reveals split work, file additional beads with dependencies. Skills guide this naturally.
+
+### Plan Requirements by Type
+
+**Bug fixes** (`type=bug`): Can proceed without plans - usually well-scoped from bug report.
+
+**Features/tasks** (`type=feature`, `type=task`): Should have plans - helps ensure design is sound before implementation.
+
+This is advisory, not enforced. Skills warn but allow override for simple changes.