Codex folder organization

[jaruesink]

Rename .claude/skills directory to .codex/skills to align with "Codex shop" branding.

This change includes renaming the directory itself and updating all internal references across documentation, scripts, and workflow definitions to reflect the new .codex/skills path.

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Summary by CodeRabbit

• Documentation

  • Updated internal skill directory references across documentation and workflow files.

• Chores

  • Reorganized skill path structure throughout the system.
  • Added optional feature hub identification step to workflow.

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Walkthrough

This change migration updates all skill directory references across the codebase from .claude/skills/ to .codex/skills/. Multiple documentation, workflow, script, and configuration files are updated to reflect the new skill directory structure. One optional workflow step is added to identify feature hubs in PR comparisons.

Changes

Cohort / File(s)	Summary
Skill Path Migration .agents/commands/update-devagent.md, .codex/skills/pr-review-integration/SKILL.md	Documentation references updated from .claude/skills/ to .codex/skills/ for skill directories.
Core Script & Workflow Updates .devagent/core/scripts/update-core.sh, .devagent/core/workflows/review-pr.md, .devagent/core/workflows/compare-prs.md	Script path literals, sparse-checkout operations, and workflow resource references changed from .claude/skills/ to .codex/skills/. Optional feature hub identification step added to compare-prs workflow.
Feature Documentation .devagent/workspace/features/completed/2025-12-25_pr-review-agent/AGENTS.md, .devagent/workspace/features/completed/2025-12-25_pr-review-agent/plan/2025-12-25_pr-review-agent-plan.md	Skill references and location paths updated; feature completion recorded with status migration from active to completed.
Research & Planning Documents .devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_*, .devagent/workspace/research/2025-12-25_workflow-vs-skill-decision-*.md	Multiple research documents and decision guides updated with .codex/skills/ paths; Agent Skill Structure location references and decision tree nodes modified accordingly.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~22 minutes

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The PR title 'Codex folder organization' clearly and concisely summarizes the main change: renaming the .claude/skills directory to .codex/skills and updating all related references throughout the codebase.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch cursor/codex-folder-organization-e0f3

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📜 Recent review details

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

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📥 Commits

Reviewing files that changed from the base of the PR and between be0927b and 5c4620b.

📒 Files selected for processing (28)

• .agents/commands/update-devagent.md
• .codex/skills/create-slash-command/SKILL.md
• .codex/skills/create-slash-command/assets/command-template.md
• .codex/skills/create-slash-command/references/command-structure.md
• .codex/skills/create-slash-command/scripts/create_command.py
• .codex/skills/create-slash-command/scripts/create_symlink.py
• .codex/skills/github-cli-operations/SKILL.md
• .codex/skills/github-cli-operations/references/commands.md
• .codex/skills/linear-mcp-integration/SKILL.md
• .codex/skills/linear-mcp-integration/references/mcp-functions.md
• .codex/skills/pr-review-integration/SKILL.md
• .codex/skills/pr-review-integration/references/patterns.md
• .codex/skills/skill-creator/SKILL.md
• .codex/skills/skill-creator/references/output-patterns.md
• .codex/skills/skill-creator/references/workflows.md
• .codex/skills/skill-creator/scripts/init_skill.py
• .codex/skills/skill-creator/scripts/package_skill.py
• .codex/skills/skill-creator/scripts/quick_validate.py
• .devagent/core/scripts/update-core.sh
• .devagent/core/workflows/compare-prs.md
• .devagent/core/workflows/review-pr.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/AGENTS.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/plan/2025-12-25_pr-review-agent-plan.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_github-linear-integration-skills.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_pr-review-approach.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_skills-review.md
• .devagent/workspace/research/2025-12-25_workflow-vs-skill-decision-guide.md
• .devagent/workspace/research/2025-12-25_workflow-vs-skill-decision-tree.md

🧰 Additional context used

📓 Path-based instructions (4)

.devagent/workspace/features/**

📄 CodeRabbit inference engine (AGENTS.md)

Store all feature work in .devagent/workspace/features/ with dated folders

Files:

• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_pr-review-approach.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_github-linear-integration-skills.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_skills-review.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/AGENTS.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/plan/2025-12-25_pr-review-agent-plan.md

.devagent/workspace/features/completed/**

📄 CodeRabbit inference engine (AGENTS.md)

Move completed features to .devagent/workspace/features/completed/

Files:

• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_pr-review-approach.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_github-linear-integration-skills.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_skills-review.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/AGENTS.md
• .devagent/workspace/features/completed/2025-12-25_pr-review-agent/plan/2025-12-25_pr-review-agent-plan.md

.devagent/workspace/research/**

📄 CodeRabbit inference engine (AGENTS.md)

Reference the constitution (.devagent/workspace/memory/constitution.md) for alignment in research packets

Files:

• .devagent/workspace/research/2025-12-25_workflow-vs-skill-decision-guide.md
• .devagent/workspace/research/2025-12-25_workflow-vs-skill-decision-tree.md

.devagent/core/workflows/**/*.md

📄 CodeRabbit inference engine (AGENTS.md)

Validate workflow definition changes against existing workflows before committing

Files:

• .devagent/core/workflows/review-pr.md
• .devagent/core/workflows/compare-prs.md

🔇 Additional comments (16)

.codex/skills/pr-review-integration/SKILL.md (1)

163-164: LGTM! Path references updated correctly.

The skill reference paths have been updated consistently to use the new .codex/skills/ directory structure.

.agents/commands/update-devagent.md (1)

8-8: LGTM! Directory reference updated correctly.

The documented directory path has been updated to reflect the new .codex/skills/ structure.

.devagent/core/workflows/compare-prs.md (2)

26-28: LGTM! Resource strategy paths updated correctly.

The skill reference paths in the Resource Strategy section have been updated to use the new .codex/skills/ directory structure.

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43-57: LGTM! Context gathering skill references updated correctly.

All skill path references in the context gathering workflow steps have been consistently updated to .codex/skills/.

.devagent/workspace/features/completed/2025-12-25_pr-review-agent/AGENTS.md (2)

24-24: LGTM! Progress log entry appropriately documents the path migration.

The progress log entry clearly documents the research completion and the new .codex/skills/ directory structure.

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54-56: LGTM! Skill reference paths updated correctly.

All skill reference documentation links have been updated to use the new .codex/skills/ directory structure.

.devagent/core/workflows/review-pr.md (2)

27-28: LGTM! Resource strategy skill paths updated correctly.

The skill reference paths in the Resource Strategy section have been updated to use the new .codex/skills/ directory structure.

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42-53: LGTM! Context gathering skill references updated correctly.

All skill path references throughout the context gathering workflow steps have been consistently updated to .codex/skills/.

.devagent/workspace/research/2025-12-25_workflow-vs-skill-decision-guide.md (1)

87-87: LGTM! Agent skill location path updated correctly.

The skill directory path in the Agent Skill Structure section has been updated to reflect the new .codex/<skill-name>/ location.

.devagent/workspace/research/2025-12-25_workflow-vs-skill-decision-tree.md (2)

26-26: LGTM! Mermaid diagram path updated correctly.

The skill directory path in the decision tree diagram has been updated to use .codex/skill-name/.

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40-40: LGTM! Skill creation path updated correctly.

The skill creation instruction in the diagram end node has been updated to reference .codex/skill-name/.

.devagent/core/scripts/update-core.sh (1)

55-100: Shell script path migration is clean and complete. All references to .claude/skills have been consistently updated to .codex/skills throughout the script, with no remaining references to the old path elsewhere in the repository. The script properly maintains conditional directory existence checks, graceful handling of missing directories with informative warnings, and correct rsync operations with the updated paths. The functional logic remains unchanged—only the path strings have been updated.

.devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_pr-review-approach.md (1)

1-339: Comprehensive skill path updates applied consistently throughout.

All references to .claude/skills/ have been correctly updated to .codex/skills/ across this research document. The document structure, cross-references, and semantic meaning are preserved. No issues identified.

.devagent/workspace/features/completed/2025-12-25_pr-review-agent/plan/2025-12-25_pr-review-agent-plan.md (1)

1-361: All skill path references updated consistently in dependencies and appendices.

Both the "Technical Notes & Dependencies" section and the "Appendices & References" section have been updated with the new .codex/skills/ paths. Status markers and plan structure remain intact.

.devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_github-linear-integration-skills.md (1)

1-180: Skill directory structure documentation updated to reflect Codex paths.

The "Agent Skills Format" section and "Repo Next Steps" section both reference .codex/skills/ paths correctly. The documentation structure remains coherent.

.devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_skills-review.md (1)

1-202: Skills inventory and assessment documentation updated consistently.

All eight skill path references (github-cli-operations, linear-mcp-integration, pr-review-integration, skill-creator) have been updated from .claude/ to .codex/ paths. The assessment logic, recommendations, and conclusions remain intact.

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