refactor(skills): migrate commands to skills directory structure

Move all 27 command .md files from commands/ to skills/*/SKILL.md
format. Claude Code 2.1.3+ merged commands and skills - both create
slash commands and work identically. Skills add optional features
like supporting files and automatic context loading.

- commands/ce/*.md -> skills/ce-*/SKILL.md
- commands/workflows/*.md -> skills/workflows-*/SKILL.md
- commands/*.md -> skills/*/SKILL.md
- Update plugin.json and marketplace.json descriptions
- Update CLAUDE.md directory structure docs
- Update deploy-docs and generate_command references

Fixes #116

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

plugins/compound-engineering/skills/deploy-docs/SKILL.md

@@ -0,0 +1,112 @@
+---
+name: deploy-docs
+description: Validate and prepare documentation for GitHub Pages deployment
+disable-model-invocation: true
+---
+
+# Deploy Documentation Command
+
+Validate the documentation site and prepare it for GitHub Pages deployment.
+
+## Step 1: Validate Documentation
+
+Run these checks:
+
+```bash
+# Count components
+echo "Agents: $(ls plugins/compound-engineering/agents/*.md | wc -l)"
+echo "Skills: $(ls -d plugins/compound-engineering/skills/*/ 2>/dev/null | wc -l)"
+
+# Validate JSON
+cat .claude-plugin/marketplace.json | jq . > /dev/null && echo "✓ marketplace.json valid"
+cat plugins/compound-engineering/.claude-plugin/plugin.json | jq . > /dev/null && echo "✓ plugin.json valid"
+
+# Check all HTML files exist
+for page in index agents commands skills mcp-servers changelog getting-started; do
+  if [ -f "plugins/compound-engineering/docs/pages/${page}.html" ] || [ -f "plugins/compound-engineering/docs/${page}.html" ]; then
+    echo "✓ ${page}.html exists"
+  else
+    echo "✗ ${page}.html MISSING"
+  fi
+done
+```
+
+## Step 2: Check for Uncommitted Changes
+
+```bash
+git status --porcelain plugins/compound-engineering/docs/
+```
+
+If there are uncommitted changes, warn the user to commit first.
+
+## Step 3: Deployment Instructions
+
+Since GitHub Pages deployment requires a workflow file with special permissions, provide these instructions:
+
+### First-time Setup
+
+1. Create `.github/workflows/deploy-docs.yml` with the GitHub Pages workflow
+2. Go to repository Settings > Pages
+3. Set Source to "GitHub Actions"
+
+### Deploying
+
+After merging to `main`, the docs will auto-deploy. Or:
+
+1. Go to Actions tab
+2. Select "Deploy Documentation to GitHub Pages"
+3. Click "Run workflow"
+
+### Workflow File Content
+
+```yaml
+name: Deploy Documentation to GitHub Pages
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'plugins/compound-engineering/docs/**'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/configure-pages@v4
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'plugins/compound-engineering/docs'
+      - uses: actions/deploy-pages@v4
+```
+
+## Step 4: Report Status
+
+Provide a summary:
+
+```
+## Deployment Readiness
+
+✓ All HTML pages present
+✓ JSON files valid
+✓ Component counts match
+
+### Next Steps
+- [ ] Commit any pending changes
+- [ ] Push to main branch
+- [ ] Verify GitHub Pages workflow exists
+- [ ] Check deployment at https://everyinc.github.io/compound-engineering-plugin/
+```