Codex: duplicate skills appear because setup installs nested SKILL.md sidecars under ~/.codex/skills/gstack

[wmzhai]

After installing gstack for Codex, Codex shows duplicate skill entries in the $ skill picker/autocomplete.

What I observed:

• Browse appeared twice
• Review, QA, and several other gstack skills also appeared twice
• The duplicates showed up even when I was working in other repositories, so this was not just a single-project .agents/skills vs global install conflict

Environment:

• gstack 0.9.0
• Codex CLI 0.116.0

Repro:

1. Install or reinstall gstack for Codex with:

   ./setup --host codex

2. Open Codex and type $ to open the skill picker/autocomplete
3. Notice that some gstack skills appear twice, especially Browse

Why this seems to happen:

• The Codex install creates top-level skills such as:
  • ~/.codex/skills/gstack-browse/SKILL.md
  • ~/.codex/skills/gstack-review/SKILL.md
  • ~/.codex/skills/gstack-qa/SKILL.md
• But it also installs a runtime sidecar at ~/.codex/skills/gstack/
• In the buggy layout, that sidecar also exposed nested skill directories/files such as:
  • ~/.codex/skills/gstack/browse/SKILL.md
  • ~/.codex/skills/gstack/review/SKILL.md
  • ~/.codex/skills/gstack/qa/SKILL.md
• So Codex ends up discovering the same logical skill from two different paths

Expected:

• Each gstack skill should appear exactly once in the Codex skill picker

Actual:

• Codex discovers duplicate gstack skills because the sidecar directory under ~/.codex/skills/gstack contains nested SKILL.md files in addition to the top-level gstack-* skills

Suggested fix:

• Keep ~/.codex/skills/gstack as a runtime sidecar only
• Do not link whole browse/, qa/, or review/ directories into it if they contain SKILL.md
• Expose only the runtime assets the generated skills actually need, for example:
  • bin/
  • browse/dist/
  • review/checklist.md
  • review/design-checklist.md
  • review/greptile-triage.md
  • review/TODOS-format.md
• Keep user-facing discoverable skills at the top level only, e.g. gstack-browse, gstack-review, gstack-qa, etc.

This looks like an installation-layout bug in gstack rather than a Codex UI bug.

[shichangs]

Fix available in #236 — migrates direct Codex installs and creates a minimal runtime root to prevent duplicate skill discovery.