fix: avoid duplicate Codex skill discovery

[shichangs]

Summary

Fix duplicate Codex skill discovery when gstack is installed directly into ~/.codex/skills/gstack.

This changes the Codex setup flow so we no longer expose the full repo under the Codex skills root, which was letting Codex recursively discover both:

• source skill directories in the repo checkout
• generated Codex skills linked at the top level

That produced duplicate entries in the skill picker because both copies shared the same name: frontmatter.

What changed

• migrate direct Codex installs from ~/.codex/skills/gstack to ~/.gstack/repos/gstack during ./setup --host codex
• create a minimal ~/.codex/skills/gstack runtime root instead of symlinking the whole repo
• keep only the runtime assets Codex skills actually need in that runtime root:
  • root SKILL.md
  • bin/
  • browse/bin
  • browse/dist
  • gstack-upgrade/SKILL.md
  • review/checklist.md, review/design-checklist.md, review/greptile-triage.md, review/TODOS-format.md (individual files, not the whole review/ dir which contains its own SKILL.md)
• update the Codex install docs to recommend cloning outside ~/.codex/skills
• add setup validation tests that lock in the new layout and migration behavior

Why this fixes the issue

Codex scans ~/.codex/skills recursively. Before this change, a direct install left the full gstack repo under ~/.codex/skills/gstack, so Codex could discover both the source SKILLs and the generated gstack-* Codex skills.

After this change:

• generated Codex skills still live at the top level in ~/.codex/skills
• ~/.codex/skills/gstack is now only a runtime sidecar, not a second discoverable skill tree
• review assets are symlinked as individual files (not the whole review/ dir) to avoid re-introducing duplicate discovery via review/SKILL.md

That removes the duplicate discovery path without changing the absolute paths referenced by generated Codex skills.

Testing

Automated

• bash -n setup ✅
• bun test test/gen-skill-docs.test.ts ✅ (88 tests pass)
• bun run gen:skill-docs --dry-run ✅
• bun run gen:skill-docs --host codex --dry-run ✅

Manual regression

• direct-install scenario:
  • cloned gstack into ~/.codex/skills/gstack
  • ran ./setup --host codex
  • verified setup migrated the repo to ~/.gstack/repos/gstack
  • verified ~/.codex/skills/gstack became a minimal runtime root
  • verified generated gstack-* Codex skills were linked at the top level
• normal-install scenario:
  • cloned gstack into a normal directory outside ~/.codex/skills
  • ran ./setup --host codex
  • verified the same clean Codex layout was produced

Not run

• bun run test:e2e
• bun run test:evals

These remain gated by the project's Tier 2 / Tier 3 eval setup.

Closes #235

[shichangs]

@wmzhai @garrytan This PR is ready for review. It fixes the duplicate Codex skill discovery issue (#235) by:

1. Migrating direct ~/.codex/skills/gstack installs to ~/.gstack/repos/gstack
2. Creating a minimal runtime root that only exposes the specific assets Codex skills need
3. Symlinking review assets as individual files (not the whole review/ dir) to avoid re-introducing duplicates via review/SKILL.md

@wmzhai — could you verify this fixes the duplicate skills you were seeing? After pulling, run ./setup --host codex and check the Codex skill picker.

[shichangs]

@garrytan Friendly ping — this is ready for review. No conflicts with main, tests included. Happy to adjust anything.