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/research-agents.md

@@ -0,0 +1,49 @@
+---
+description: How to spawn and coordinate research sub-agents
+---
+
+# Research Agents
+
+Use parallel sub-agents for efficient codebase research.
+
+## Available Agents
+
+| Agent | Purpose |
+|-------|---------|
+| codebase-locator | Find WHERE files and components live |
+| codebase-analyzer | Understand HOW specific code works |
+| codebase-pattern-finder | Find examples of existing patterns |
+| thoughts-locator | Discover relevant documents in thoughts/ |
+
+## Spawning Protocol
+
+1. **Decompose** - Break the research question into 3-5 specific questions
+2. **Spawn parallel** - Use one Task call with multiple agents
+3. **Be specific** - Include directories and file patterns in prompts
+4. **Wait for all** - Do not synthesize until ALL agents complete
+5. **Synthesize** - Combine findings into coherent summary with file:line references
+
+## Example
+
+```
+Task(codebase-locator, "Find all files related to authentication in src/")
+Task(codebase-analyzer, "Explain how JWT tokens are validated in src/auth/")
+Task(codebase-pattern-finder, "Find examples of middleware patterns in src/")
+Task(thoughts-locator, "Find documents about auth design decisions in thoughts/")
+```
+
+## Key Principles
+
+- **Parallel when different** - Run agents in parallel when searching for different things
+- **WHAT not HOW** - Each agent knows its job; tell it what you need, not how to search
+- **Document, don't evaluate** - Agents should describe what exists, not critique it
+- **Specific directories** - Always scope searches to relevant directories
+- **File references** - Include specific file:line references in synthesis
+
+## Agent Prompts
+
+When spawning agents, include:
+- The specific question or goal
+- Relevant directories to search
+- Reminder to document (not evaluate) what they find
+- Request for file:line references in findings