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>

home/roles/development/skills/micro/artifact-format.md

@@ -0,0 +1,123 @@
+---
+description: How to structure research and plan artifacts in thoughts/
+---
+
+# Artifact Format
+
+Standardized format for thoughts/ artifacts. All beads-related artifacts should follow these conventions for consistency and machine parseability.
+
+## Frontmatter (Required)
+
+Every artifact MUST include YAML frontmatter:
+
+```yaml
+---
+date: 2026-01-15T10:00:00-08:00  # ISO 8601 with timezone
+bead_id: project-abc              # Bead identifier
+bead_title: "Title of the bead"   # Human-readable title
+author: claude                    # Who created this
+git_commit: abc123def             # Commit hash at creation
+branch: main                      # Branch name
+repository: repo-name             # Repository name
+status: draft|complete            # Artifact status
+---
+```
+
+### Gathering Metadata
+
+```bash
+git rev-parse HEAD                           # Current commit
+git branch --show-current                    # Current branch
+basename $(git rev-parse --show-toplevel)    # Repo name
+date -Iseconds                               # ISO timestamp
+```
+
+## Research Artifact Structure
+
+Location: `thoughts/beads-{bead-id}/research.md`
+
+```markdown
+# Research: {bead title}
+
+**Bead**: {bead-id}
+**Date**: {timestamp}
+**Git Commit**: {commit hash}
+
+## Research Question
+{Original question from bead description}
+
+## Summary
+{2-3 sentence overview answering the research question}
+
+## Key Discoveries
+- {Finding with file:line reference}
+- {Pattern or convention found}
+- {Architectural decision documented}
+
+## Architecture
+{Current patterns and conventions in the codebase}
+
+## Code References
+- `path/to/file.py:123` - Description of relevance
+- `another/file.ts:45-67` - Description of relevance
+
+## Open Questions
+{Areas needing further investigation or human clarification}
+```
+
+## Plan Artifact Structure
+
+Location: `thoughts/beads-{bead-id}/plan.md`
+
+```markdown
+# {Title} Implementation Plan
+
+## Overview
+{What we're implementing and why - 1-2 sentences}
+
+## Current State
+{What exists now, key constraints discovered}
+
+### Key Discoveries
+- {Finding with file:line reference}
+- {Pattern to follow}
+
+## Desired End State
+{Specification of what success looks like}
+
+## What We're NOT Doing
+{Explicitly list out-of-scope items}
+
+## Phase 1: {Descriptive Name}
+
+### Overview
+{What this phase accomplishes}
+
+### Changes
+- [ ] {Specific change with file path}
+- [ ] {Another change}
+
+### Success Criteria
+
+#### Automated
+- [ ] Tests pass: `{test command}`
+- [ ] Lint passes: `{lint command}`
+
+#### Manual
+- [ ] {Human verification step}
+
+## Phase 2: {Descriptive Name}
+{Repeat structure...}
+
+## References
+- Bead: {bead-id}
+- Research: `thoughts/beads-{bead-id}/research.md`
+```
+
+## Key Principles
+
+1. **Always include file:line references** - Makes artifacts actionable
+2. **Separate automated vs manual verification** - Enables agent autonomy
+3. **Use checkboxes for phases** - Enables resumability after interruption
+4. **Keep frontmatter machine-parseable** - Enables tooling integration
+5. **Link related artifacts** - Research links to plan, plan links to bead