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/default.nix

@@ -90,8 +90,8 @@ in
         fi
       done
 
-      # Copy local skills from this repo (with retry for race conditions with running Claude)
-      for file in ${./skills}/*.md; do
+      # Copy local commands from this repo (with retry for race conditions with running Claude)
+      for file in ${./commands}/*.md; do
         if [ -f "$file" ]; then
           filename=$(basename "$file" .md)
           dest="$HOME/.claude/commands/''${filename}.md"
@@ -104,11 +104,36 @@ in
         fi
       done
 
-      $DRY_RUN_CMD echo "Claude Code humanlayer commands and agents installed successfully${
-        if cfg.allowArbitraryClaudeCodeModelSelection
-        then " (model specifications preserved)"
-        else " (model selection removed)"
-      } + local skills"
+      # Copy local skills (reference materials) to skills subdirectory
+      mkdir -p ~/.claude/commands/skills
+      for file in ${./skills}/*.md; do
+        if [ -f "$file" ]; then
+          filename=$(basename "$file" .md)
+          dest="$HOME/.claude/commands/skills/''${filename}.md"
+          rm -f "$dest" 2>/dev/null || true
+          if ! cp "$file" "$dest" 2>/dev/null; then
+            sleep 0.5
+            cp "$file" "$dest" || echo "Warning: Failed to copy $filename.md to skills"
+          fi
+        fi
+      done
+
+      # Copy micro-skills (compact reusable knowledge referenced by formulas)
+      for file in ${./skills/micro}/*.md; do
+        if [ -f "$file" ]; then
+          cp "$file" "$HOME/.claude/commands/skills/$(basename "$file")"
+        fi
+      done
+
+      # Install beads formulas to user-level formula directory
+      mkdir -p ~/.beads/formulas
+      for file in ${./formulas}/*.formula.toml; do
+        if [ -f "$file" ]; then
+          cp "$file" "$HOME/.beads/formulas/$(basename "$file")"
+        fi
+      done
+
+      $DRY_RUN_CMD echo "Claude Code plugins installed: humanlayer commands/agents + local commands + local skills + formulas"
     '';
 
     # Set up beads Claude Code integration (hooks for SessionStart/PreCompact)