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.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: