fix(#1326): stop emitting Codex agents/openai.yaml sidecars; clean up stale ones (#1360)

* fix(#1326): stop emitting Codex agents/openai.yaml sidecars; clean up stale ones

Codex installs wrote an agents/openai.yaml sidecar under every managed gsd-*
skill dir. Recent Codex builds index both SKILL.md and the sidecar, so each
GSD skill appeared twice in autocomplete (canonical gsd-* name + humanized
display_name).

- Replace writeCodexSkillMetadataFiles / generateCodexSkillMetadataYaml with
  cleanupCodexSkillMetadataSidecars: Codex-only (if isCodex), removes stale
  managed gsd-*/agents/openai.yaml and prunes the now-empty agents/ dir.
- Preserve user-owned dirs (gsd-dev-preferences), non-empty agents/ dirs, and
  non-gsd dirs; lstat-guard against symlinked agents/ so a delete can never
  escape the skills tree; fail-open per directory.
- Codex relies on SKILL.md alone for /skills discovery.
- Update USER-GUIDE/FEATURES docs and rewrite the #774 emission tests into
  cleanup tests.

Scope: the sidecar duplicate only. The separate multi-root (~/.agents/skills
shared-skills) duplicate facet is a distinct concern, not addressed here.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* chore(#1326): add changeset for Codex sidecar cleanup

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

docs/USER-GUIDE.md

@@ -731,13 +731,13 @@ To assign different models on a non-Claude runtime:
 
 #### Codex skill picker and agent scheduling (#774)
 
-GSD enriches each Codex install with two additional artifacts:
-
-- **Skill TUI chip** — each installed `gsd-*` skill directory contains an `agents/openai.yaml` file that populates the Codex `/skills` picker with a human-readable display name and a short description, so you can browse and invoke GSD skills from the Codex TUI without typing the full skill name.
+GSD enriches each Codex install with an additional artifact:
 
 - **Flex-tier scheduling** — light-tier agents (haiku-equivalent) emit `service_tier = "flex"` and `model_verbosity = "low"` in their agent TOML. The Codex scheduler routes these agents to the flex tier (lower cost, background processing) and suppresses verbose token output.
 
-Both enrichments are written automatically at install time and require no manual configuration. Requires Codex CLI ≥ 0.130.0.
+GSD skills appear in the Codex `/skills` picker via their `SKILL.md` file, which Codex discovers automatically. No `agents/openai.yaml` sidecar is emitted — doing so caused duplicate autocomplete entries (#1326).
+
+This enrichment is written automatically at install time and requires no manual configuration. Requires Codex CLI ≥ 0.130.0.
 
 #### Switching from Claude to Codex with one config change (#2517)