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>

Author: mvanhorn

.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",

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",

plugins/compound-engineering/CLAUDE.md

@@ -34,15 +34,16 @@ agents/
 ├── workflow/   # Workflow automation agents
 └── docs/       # Documentation agents
 
-commands/
-├── ce/         # Core workflow commands (ce:plan, ce:review, etc.)
-├── workflows/  # Deprecated aliases for ce:* commands
-└── *.md        # Utility commands
-
 skills/
-└── *.md        # All skills at root level
+├── ce-*/          # Core workflow skills (ce:plan, ce:review, etc.)
+├── workflows-*/   # Deprecated aliases for ce:* skills
+└── */             # All other skills
 ```
 
+> **Note:** Commands were migrated to skills in v2.39.0. All former
+> `/command-name` slash commands now live under `skills/command-name/SKILL.md`
+> and work identically (Claude Code 2.1.3+ merged the two formats).
+
 ## Command Naming Convention
 
 **Workflow commands** use `ce:` prefix to unambiguously identify them as compound-engineering commands: