Consolidate repository skill installation paths

[davidsneighbour]

Current behaviour

Repository-local skills are split across .agents/skills, .codex/skills, and .claude/skills. Some tool-specific skill directories contain full skill copies instead of symlinks back to .agents/skills.

skills-lock.json and npx skills add/update should have a single installation target so future updates do not mutate tool-specific symlink directories.

Expected behaviour

• .agents/skills is the only real repository-local skill directory.
• .codex/skills and .claude/skills contain only symlinks to .agents/skills.
• npm scripts for skills installation and updates pass the local .agents/skills target explicitly.
• Existing real tool-specific skill copies are moved or mirrored into .agents/skills before being replaced by symlinks.

Notes

This follows the existing AGENTS.md and CLAUDE.md guidance that tool-specific skill directories should only surface .agents/skills.