[codex] Avoid shadowing user skills in lab setup

[samsja]

Summary

prime lab setup now treats .prime/skills as the shared Lab skills source and avoids installing project-level agent skill links that would shadow same-name user-scope skills.

Problem

The setup flow downloaded bundled Lab skills to .prime/skills, then linked/copied them into agent-specific project directories such as .codex/skills. If a user already had a same-name skill in ~/.codex/skills, the project skill could take precedence and effectively override the user's skill.

Changes

• Link agent skill roots to .prime/skills when there are no user-scope conflicts.
• Detect user-scope skill conflicts before creating project links.
• Remove old managed project skill links on rerun when they would shadow a user skill.
• Fall back to per-skill links for non-conflicting skills when conflicts exist.
• Only write CLAUDE.md when claude is one of the selected agents.
• Add setup tests for user-scope conflict handling and Claude-specific file generation.

Validation

• uv run pytest tests/test_setup_script.py -> 17 passed
• uv run ruff check verifiers/scripts/setup.py tests/test_setup_script.py -> passed

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Note

Medium Risk
Changes how prime lab setup creates agent skill directories and symlinks, including deleting previously-managed symlinks; mistakes could remove/skip intended project skills or create incorrect links on reruns.

Overview
prime lab setup now detects user-scoped agent skills (e.g. ~/.codex/skills) and avoids creating project-level links in .codex/skills that would shadow them; when conflicts exist it removes only previously-managed symlinks and skips conflicting skills while still materializing non-conflicting ones.

When there are no user conflicts (and no skill-name mapping), the setup prefers linking the agent’s skills root directly to .prime/skills. It also only downloads CLAUDE.md when claude is among the selected agents, and adds targeted tests covering HOME isolation, user-skill conflict handling, and Claude-specific file generation.

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[willccbb]

@cursoragent fix ruff pls

[cursor]

• Ran Ruff locally; the failure was from formatting. Applied uvx ruff format to verifiers/scripts/setup.py.

• Verified both checks pass:

  • uvx ruff check . → All checks passed
  • uvx ruff format --check . → 310 files already formatted

• Committed and pushed: style(ruff): format setup script to satisfy ruff format --check (branch fix/lab-skill-user-scope-precedence). The PR should now pass the Ruff job.