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/formulas/rpi.formula.toml

@@ -0,0 +1,124 @@
+# RPI Formula - Research -> Plan -> Implement
+#
+# Universal workflow for feature development with human gates.
+
+formula = "rpi"
+description = """
+Research -> Plan -> Implement workflow.
+
+Usage:
+  bd pour rpi --var title="Add user preferences"
+  bd pour rpi --var title="Auth" --var bead_id="project-abc" --var test_cmd="nix flake check"
+"""
+version = 1
+type = "workflow"
+
+# ─── Variables ───
+
+[vars.title]
+required = true
+description = "What are we building?"
+
+[vars.bead_id]
+description = "Existing bead ID (creates new if not provided)"
+
+[vars.test_cmd]
+default = "make test"
+description = "Command to run tests"
+
+[vars.lint_cmd]
+default = "make lint"
+description = "Command to run linting"
+
+# ─── Research Phase ───
+
+[[steps]]
+id = "research"
+title = "Research: {{title}}"
+skill = "research-agents"
+description = """
+Conduct comprehensive codebase research.
+
+Goals:
+- Understand current implementation
+- Identify patterns to follow
+- Find relevant files and dependencies
+- Document key discoveries
+
+Output: thoughts/beads-{{bead_id}}/research.md
+"""
+
+# ─── Planning Phase ───
+
+[[steps]]
+id = "plan"
+title = "Plan: {{title}}"
+needs = ["research"]
+type = "human"
+skill = "planning"
+description = """
+Create detailed implementation plan based on research.
+
+Goals:
+- Present understanding and clarify requirements
+- Propose design options with tradeoffs
+- Define phases with success criteria
+- Identify what we're NOT doing
+
+Output: thoughts/beads-{{bead_id}}/plan.md
+"""
+
+[steps.gate]
+type = "human"
+reason = "Plan approval before implementation"
+
+# ─── Implementation Phase ───
+
+[[steps]]
+id = "implement"
+title = "Implement: {{title}}"
+needs = ["plan"]
+description = """
+Execute the approved plan phase by phase.
+
+For each phase:
+1. Make the changes
+2. Run verification: {{test_cmd}}, {{lint_cmd}}
+3. Update plan checkboxes for resumability
+
+Stop and ask if encountering unexpected issues.
+"""
+
+# ─── Verification Phase ───
+
+[[steps]]
+id = "verify"
+title = "Manual verification"
+needs = ["implement"]
+type = "human"
+description = """
+Human confirms implementation works correctly.
+
+Check: feature works, edge cases handled, no regressions.
+Tests: {{test_cmd}} | Lint: {{lint_cmd}}
+"""
+
+[steps.gate]
+type = "human"
+reason = "Confirm implementation is correct"
+
+# ─── Completion ───
+
+[[steps]]
+id = "complete"
+title = "Close bead"
+needs = ["verify"]
+skill = "artifact-format"
+description = """
+Mark work as complete.
+
+Actions:
+- bd update {{bead_id}} --notes="Implementation complete"
+- bd close {{bead_id}} --reason="Completed: {{title}}"
+- bd sync && git push
+"""