refactor(skills): migrate commands to skills directory structure

[mvanhorn]

Summary

Fixes #116

Migrates all 27 command files from commands/ to skills/*/SKILL.md format, as Claude Code 2.1.3+ merged commands and skills into a unified system. All slash commands (e.g., /ce:plan, /lfg, /changelog) continue to work identically since skills with the same name: frontmatter create the same slash commands.

Changes

• Move commands/ce/*.md to skills/ce-*/SKILL.md (5 core workflow skills)
• Move commands/workflows/*.md to skills/workflows-*/SKILL.md (5 deprecated aliases)
• Move commands/*.md to skills/*/SKILL.md (17 utility skills)
• Remove empty commands/ directory
• Update plugin.json and marketplace.json descriptions (29 agents, 47 skills)
• Update CLAUDE.md directory structure documentation
• Update deploy-docs and generate_command skill references

Testing

• bun test - all 313 tests pass
• Slash command names preserved via name: frontmatter (e.g., name: ce:plan in skills/ce-plan/SKILL.md)
• Deprecated workflows:* aliases preserved (e.g., name: workflows:plan in skills/workflows-plan/SKILL.md)

This contribution was developed with AI assistance (Claude Code).

[kieranklaassen]

need to check this for other tools too but yes I think we shoudl do this. I think @tmchow also has ideas and plans

[mvanhorn]

Thanks for the green light! Happy to coordinate with @tmchow if there's a specific direction in mind - I can adjust the PR or hold off until the broader plan is clear.

[tmchow]

@mvanhorn I’m inclined to just go with it and not wait for my future plotting. lemme review it and think on it for a beat.

[tmchow]

Thanks for the green light! Happy to coordinate with @tmchow if there's a specific direction in mind - I can adjust the PR or hold off until the broader plan is clear.

@mvanhorn @kieranklaassen I'm good with this one after reviewing it. @mvanhorn can you resolve the branch conflicts?

[tmchow]

lgtm

[mvanhorn]

Branch conflicts resolved - rebased on latest main and bumped version to 2.40.0. Ready for merge.