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>

.claude-plugin/marketplace.json

@@ -11,8 +11,8 @@
   "plugins": [
     {
       "name": "compound-engineering",
-      "description": "AI-powered development tools that get smarter with every use. Make each unit of engineering work easier than the last. Includes 28 specialized agents, 22 commands, and 20 skills.",
-      "version": "2.39.0",
+      "description": "AI-powered development tools that get smarter with every use. Make each unit of engineering work easier than the last. Includes 28 specialized agents and 47 skills.",
+      "version": "2.40.0",
       "author": {
         "name": "Kieran Klaassen",
         "url": "https://github.com/kieranklaassen",