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/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "compound-engineering",
-  "version": "2.39.0",
-  "description": "AI-powered development tools. 28 agents, 22 commands, 20 skills, 1 MCP server for code review, research, design, and workflow automation.",
+  "version": "2.40.0",
+  "description": "AI-powered development tools. 28 agents, 47 skills, 1 MCP server for code review, research, design, and workflow automation.",
   "author": {
     "name": "Kieran Klaassen",
     "email": "kieran@every.to",