refactor: consolidate commands into skills and clean up stale references

Remove legacy commands/ directory (all 7 commands already exist as skills),
delete ghost ai-dlc-intent-detection skill and redundant methodology skill,
and fix stale /plan and /done references in ai-dlc-fundamentals.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: jwaldrip