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",

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:

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

@@ -15,7 +15,6 @@ Run these checks:
 ```bash
 # Count components
 echo "Agents: $(ls plugins/compound-engineering/agents/*.md | wc -l)"
-echo "Commands: $(ls plugins/compound-engineering/commands/*.md | wc -l)"
 echo "Skills: $(ls -d plugins/compound-engineering/skills/*/ 2>/dev/null | wc -l)"
 
 # Validate JSON

plugins/compound-engineering/skills/generate_command/SKILL.md

@@ -7,7 +7,7 @@ disable-model-invocation: true
 
 # Create a Custom Claude Code Command
 
-Create a new slash command in `.claude/commands/` for the requested task.
+Create a new skill in `.claude/skills/` for the requested task.
 
 ## Goal
 
@@ -128,10 +128,10 @@ Implement #$ARGUMENTS following these steps:
 
 ## Creating the Command File
 
-1. **Create the file** at `.claude/commands/[name].md` (subdirectories like `workflows/` supported)
+1. **Create the directory** at `.claude/skills/[name]/SKILL.md`
 2. **Start with YAML frontmatter** (see section above)
-3. **Structure the command** using the template above
-4. **Test the command** by using it with appropriate arguments
+3. **Structure the skill** using the template above
+4. **Test the skill** by using it with appropriate arguments
 
 ## Command File Template