Codex folder organization

.agents/commands/update-devagent.md

@@ -5,7 +5,7 @@
 1. Run the DevAgent core update script located at `.devagent/core/scripts/update-core.sh` to update core files, commands, and skills from the DevAgent repository.
 
 2. After the script completes successfully, provide a summary of what was updated, including:
-   - Which directories were updated (`.devagent/core/`, `.agents/commands/`, `.claude/skills/`)
+   - Which directories were updated (`.devagent/core/`, `.agents/commands/`, `.codex/skills/`)
    - Any specific skills or commands that were updated
    - Any backup information (if kept)
    - Note that changes were NOT committed (as per user preference)

.claude/skills/pr-review-integration/SKILL.md → .codex/skills/pr-review-integration/SKILL.md

@@ -160,5 +160,5 @@ mcp_Linear_update_issue({
 ## Reference Documentation
 
 - **Review Patterns**: See [patterns.md](references/patterns.md) for detailed patterns, edge cases, and checklist templates
-- **GitHub CLI Operations**: `.claude/skills/github-cli-operations/SKILL.md` - GitHub CLI patterns
-- **Linear MCP Integration**: `.claude/skills/linear-mcp-integration/SKILL.md` - Linear MCP functions
+- **GitHub CLI Operations**: `.codex/skills/github-cli-operations/SKILL.md` - GitHub CLI patterns
+- **Linear MCP Integration**: `.codex/skills/linear-mcp-integration/SKILL.md` - Linear MCP functions

.devagent/core/scripts/update-core.sh

@@ -52,18 +52,18 @@ git config core.sparseCheckout true
 git config index.sparse true
 echo "$CORE_PATH/" >> .git/info/sparse-checkout
 echo ".agents/" >> .git/info/sparse-checkout
-echo ".claude/skills/" >> .git/info/sparse-checkout
+echo ".codex/skills/" >> .git/info/sparse-checkout
 git pull origin main --quiet --depth=1
 
 # Ensure sparse checkout is applied (sometimes needs explicit checkout)
 git sparse-checkout reapply 2>/dev/null || true
 
 # Debug: verify what was checked out
-if [ ! -d "$TEMP_DIR/.claude/skills" ]; then
-    echo "Warning: .claude/skills directory not found in repository after checkout."
+if [ ! -d "$TEMP_DIR/.codex/skills" ]; then
+    echo "Warning: .codex/skills directory not found in repository after checkout."
     echo "This may be expected if skills haven't been added to the repository yet."
-    echo "Checking if .claude directory exists..."
-    ls -la "$TEMP_DIR/.claude" 2>/dev/null || echo "  .claude directory not found in repository."
+    echo "Checking if .codex directory exists..."
+    ls -la "$TEMP_DIR/.codex" 2>/dev/null || echo "  .codex directory not found in repository."
 fi
 
 # Merge updated core into project; overwrite upstream files, keep local additions
@@ -77,27 +77,27 @@ if [ -d "$TEMP_DIR/.agents/commands" ]; then
     echo "Updated .agents/commands directory from repository."
 fi
 
-# Merge .claude/skills directory if it exists in the repository
+# Merge .codex/skills directory if it exists in the repository
 # Only overwrite skills that exist in the source, keep other skills in target untouched
-if [ -d "$TEMP_DIR/.claude/skills" ]; then
-    mkdir -p "$PROJECT_ROOT/.claude/skills"
+if [ -d "$TEMP_DIR/.codex/skills" ]; then
+    mkdir -p "$PROJECT_ROOT/.codex/skills"
     SKILLS_UPDATED=0
     # Iterate through each skill directory, only updating skills that exist in source
     # Use find to handle cases where directory might be empty or have hidden files
     while IFS= read -r skill_dir; do
         [ -n "$skill_dir" ] || continue
         skill_name=$(basename "$skill_dir")
-        rsync -a "$skill_dir/" "$PROJECT_ROOT/.claude/skills/$skill_name/"
+        rsync -a "$skill_dir/" "$PROJECT_ROOT/.codex/skills/$skill_name/"
         SKILLS_UPDATED=$((SKILLS_UPDATED + 1))
         echo "  Updated skill: $skill_name"
-    done < <(find "$TEMP_DIR/.claude/skills" -mindepth 1 -maxdepth 1 -type d 2>/dev/null)
+    done < <(find "$TEMP_DIR/.codex/skills" -mindepth 1 -maxdepth 1 -type d 2>/dev/null)
     if [ $SKILLS_UPDATED -gt 0 ]; then
-        echo "Updated $SKILLS_UPDATED skill(s) in .claude/skills directory."
+        echo "Updated $SKILLS_UPDATED skill(s) in .codex/skills directory."
     else
         echo "No skills found in repository to update."
     fi
 else
-    echo "Note: .claude/skills directory not found in repository (may not exist yet)."
+    echo "Note: .codex/skills directory not found in repository (may not exist yet)."
 fi
 
 # Cleanup temp dir

.devagent/core/workflows/compare-prs.md

@@ -23,8 +23,8 @@ Follow standard execution directive in `.devagent/core/AGENTS.md` → Standard W
 ## Resource Strategy
 - **Comparison artifacts:** `.devagent/workspace/reviews/YYYY-MM-DD_pr-comparison_<pr-numbers>.md` — storage for PR comparison artifacts.
 - **Comparison template:** `.devagent/core/templates/pr-comparison-template.md` — template for consistent comparison format.
-- **GitHub CLI Operations Skill:** `.claude/skills/github-cli-operations/` — **Consult this skill for detailed GitHub CLI command patterns, examples, and best practices.** Use for PR operations (view PR details, get diff, extract Linear issue references, fetch review comments). The skill contains comprehensive command reference and usage patterns.
-- **Linear MCP Integration Skill:** `.claude/skills/linear-mcp-integration/` — **Consult this skill for Linear MCP function usage patterns and examples.** Use for Linear issue operations (get issue details, fetch requirements, update issues, post comments). The skill contains MCP function reference and integration patterns.
+- **GitHub CLI Operations Skill:** `.codex/skills/github-cli-operations/` — **Consult this skill for detailed GitHub CLI command patterns, examples, and best practices.** Use for PR operations (view PR details, get diff, extract Linear issue references, fetch review comments). The skill contains comprehensive command reference and usage patterns.
+- **Linear MCP Integration Skill:** `.codex/skills/linear-mcp-integration/` — **Consult this skill for Linear MCP function usage patterns and examples.** Use for Linear issue operations (get issue details, fetch requirements, update issues, post comments). The skill contains MCP function reference and integration patterns.
 - **Project standards:** `.devagent/core/AGENTS.md` (workflow guidelines), `.cursorrules` or workspace rules (code style), `.devagent/workspace/memory/constitution.md` (principles).
 - **Feature hubs:** `.devagent/workspace/features/{status}/YYYY-MM-DD_feature-slug/` — optional linking for feature-scoped comparisons.
 - **Code repository:** Analyze code changes via GitHub CLI diff and file inspection.
@@ -40,20 +40,20 @@ Follow standard execution directive in `.devagent/core/AGENTS.md` → Standard W
    - Identify common task/feature: extract from PR descriptions, Linear issues, or use provided task description
 
 2. **Context gathering (for each PR):**
-   - **Fetch PR details** using GitHub CLI (see `.claude/skills/github-cli-operations/` for detailed command patterns):
+   - **Fetch PR details** using GitHub CLI (see `.codex/skills/github-cli-operations/` for detailed command patterns):
      - Get PR title, body, author, state, base/head refs: `gh pr view <pr-number> --json title,body,author,state,baseRefName,headRefName`
      - Get changed files: `gh pr view <pr-number> --json files --jq '.files[].path'`
      - Get PR diff: `gh pr diff <pr-number>`
      - Get PR size metrics: `gh pr view <pr-number> --json additions,deletions,changedFiles`
-   - **Fetch PR review comments** using GitHub CLI (see `.claude/skills/github-cli-operations/` for comment fetching patterns):
+   - **Fetch PR review comments** using GitHub CLI (see `.codex/skills/github-cli-operations/` for comment fetching patterns):
      - Get review comments: `gh pr view <pr-number> --json reviews,comments --jq '.reviews[] | select(.state != "APPROVED") | {state, body, author}'`
      - Get PR review thread comments: `gh api repos/:owner/:repo/pulls/<pr-number>/comments` (if available)
      - Analyze comment importance: identify blocking comments, critical comments, and minor comments
      - Count comments by category for scoring
-   - **Extract Linear issue references** from PR (see `.claude/skills/github-cli-operations/` for extraction patterns):
+   - **Extract Linear issue references** from PR (see `.codex/skills/github-cli-operations/` for extraction patterns):
      - Search PR title and body for Linear issue patterns (e.g., `LIN-123`, `[LIN-123]`)
      - Extract all issue IDs found
-   - **Fetch Linear issue requirements** (if issues found; see `.claude/skills/linear-mcp-integration/` for MCP function usage):
+   - **Fetch Linear issue requirements** (if issues found; see `.codex/skills/linear-mcp-integration/` for MCP function usage):
      - For each Linear issue ID, use Linear MCP to get issue details: `mcp_Linear_get_issue({ id: "LIN-123", includeRelations: true })`
      - Extract acceptance criteria from issue description
      - Parse requirements, checkboxes, and feature specifications

.devagent/core/workflows/review-pr.md

@@ -24,8 +24,8 @@ Follow standard execution directive in `.devagent/core/AGENTS.md` → Standard W
 ## Resource Strategy
 - **Review artifacts:** `.devagent/workspace/reviews/YYYY-MM-DD_pr-<number>-review.md` — storage for all PR review artifacts.
 - **Review artifact template:** `.devagent/core/templates/review-artifact-template.md` — template for consistent review format.
-- **GitHub CLI Operations Skill:** `.claude/skills/github-cli-operations/` — **Consult this skill for detailed GitHub CLI command patterns, examples, and best practices.** Use for PR operations (view PR details, get diff, extract Linear issue references, fetch review comments). The skill contains comprehensive command reference and usage patterns.
-- **Linear MCP Integration Skill:** `.claude/skills/linear-mcp-integration/` — **Consult this skill for Linear MCP function usage patterns and examples.** Use for Linear issue operations (get issue details, fetch requirements, update issues, post comments). The skill contains MCP function reference and integration patterns.
+- **GitHub CLI Operations Skill:** `.codex/skills/github-cli-operations/` — **Consult this skill for detailed GitHub CLI command patterns, examples, and best practices.** Use for PR operations (view PR details, get diff, extract Linear issue references, fetch review comments). The skill contains comprehensive command reference and usage patterns.
+- **Linear MCP Integration Skill:** `.codex/skills/linear-mcp-integration/` — **Consult this skill for Linear MCP function usage patterns and examples.** Use for Linear issue operations (get issue details, fetch requirements, update issues, post comments). The skill contains MCP function reference and integration patterns.
 - **Project standards:** `.devagent/core/AGENTS.md` (workflow guidelines), `.cursorrules` or workspace rules (code style), `.devagent/workspace/memory/constitution.md` (principles).
 - **Feature hubs:** `.devagent/workspace/features/{status}/YYYY-MM-DD_feature-slug/` — optional linking for feature-scoped reviews.
 - **Code repository:** Analyze code changes via GitHub CLI diff and file inspection.
@@ -39,18 +39,18 @@ Follow standard execution directive in `.devagent/core/AGENTS.md` → Standard W
    - Confirm review artifact template exists
 
 2. **Context gathering:**
-   - **Fetch PR details** using GitHub CLI (see `.claude/skills/github-cli-operations/` for detailed command patterns):
+   - **Fetch PR details** using GitHub CLI (see `.codex/skills/github-cli-operations/` for detailed command patterns):
      - Get PR title, body, author, state, base/head refs: `gh pr view <pr-number> --json title,body,author,state,baseRefName,headRefName`
      - Get changed files: `gh pr view <pr-number> --json files --jq '.files[].path'`
      - Get PR diff: `gh pr diff <pr-number>`
-   - **Fetch PR review comments** using GitHub CLI (see `.claude/skills/github-cli-operations/` for comment fetching patterns):
+   - **Fetch PR review comments** using GitHub CLI (see `.codex/skills/github-cli-operations/` for comment fetching patterns):
      - Get review comments: `gh pr view <pr-number> --json reviews,comments --jq '.reviews[] | select(.state != "APPROVED") | {state, body, author}'`
      - Get PR review thread comments: `gh api repos/:owner/:repo/pulls/<pr-number>/comments` (if available)
      - Analyze comment importance: identify blocking comments (e.g., "blocking", "must fix", "critical"), critical comments (e.g., "important", "should fix"), and minor comments (e.g., "nice to have", "optional")
-   - **Extract Linear issue references** from PR (see `.claude/skills/github-cli-operations/` for extraction patterns):
+   - **Extract Linear issue references** from PR (see `.codex/skills/github-cli-operations/` for extraction patterns):
      - Search PR title and body for Linear issue patterns (e.g., `LIN-123`, `[LIN-123]`)
      - Extract all issue IDs found
-   - **Fetch Linear issue requirements** (if issues found; see `.claude/skills/linear-mcp-integration/` for MCP function usage):
+   - **Fetch Linear issue requirements** (if issues found; see `.codex/skills/linear-mcp-integration/` for MCP function usage):
      - For each Linear issue ID, use Linear MCP to get issue details: `mcp_Linear_get_issue({ id: "LIN-123", includeRelations: true })`
      - Extract acceptance criteria from issue description
      - Parse requirements, checkboxes, and feature specifications

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

@@ -21,7 +21,7 @@ Agent that reviews pull requests by analyzing code changes, checking attached Li
 
 ## Progress Log
 - [2025-12-25] Event: Feature hub scaffolded via `devagent new-feature`. Initial structure created with research/, plan/, and tasks/ directories.
-- [2025-12-25] Event: Research completed on GitHub and Linear integration skills. Created research document and three Agent Skills for GitHub CLI operations, Linear MCP integration, and PR review integration patterns. See research/2025-12-25_github-linear-integration-skills.md and .claude/skills/ directory.
+- [2025-12-25] Event: Research completed on GitHub and Linear integration skills. Created research document and three Agent Skills for GitHub CLI operations, Linear MCP integration, and PR review integration patterns. See research/2025-12-25_github-linear-integration-skills.md and .codex/skills/ directory.
 - [2025-12-25] Event: Research completed on PR review approach and architecture. Analyzed workflow vs skill decision, review process design, and integration patterns. Recommendation: Create DevAgent workflow (`devagent review-pr`) that uses existing skills for tool operations while producing structured artifacts. See research/2025-12-25_pr-review-approach.md.
 - [2025-12-25] Event: Implementation plan created via `devagent create-plan`. Plan includes 5 implementation tasks covering template creation, workflow definition, command file, documentation updates, and testing. See plan/2025-12-25_pr-review-agent-plan.md.
 - [2025-12-25] Event: Implementation completed. All 5 tasks finished: review artifact template created (`.devagent/core/templates/review-artifact-template.md`), workflow definition created (`.devagent/core/workflows/review-pr.md`), command file created (`.agents/commands/review-pr.md`), workflow roster updated (`.devagent/core/AGENTS.md`), and reviews directory structure created (`.devagent/workspace/reviews/`). Workflow is ready for testing.
@@ -51,9 +51,9 @@ Agent that reviews pull requests by analyzing code changes, checking attached Li
 - Review Progress Workflow: `.devagent/core/workflows/review-progress.md` (2025-12-25) — Related workflow for progress tracking and code verification patterns
 - Feature Directory Structure: `.devagent/workspace/features/README.md` (2025-12-25) — Standard structure for feature hubs and artifact organization
 - **Research: GitHub/Linear Integration Skills**: `.devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_github-linear-integration-skills.md` (2025-12-25) — Research on GitHub and Linear integration options and skill design
-- **GitHub CLI Operations Skill**: `.claude/skills/github-cli-operations/SKILL.md` (2025-12-25) — Agent skill for GitHub CLI operations and PR management
-- **Linear MCP Integration Skill**: `.claude/skills/linear-mcp-integration/SKILL.md` (2025-12-25) — Agent skill for Linear MCP functions and issue management
-- **PR Review Integration Skill**: `.claude/skills/pr-review-integration/SKILL.md` (2025-12-25) — Combined patterns for PR review workflows integrating GitHub and Linear (to be evaluated/repurposed)
+- **GitHub CLI Operations Skill**: `.codex/skills/github-cli-operations/SKILL.md` (2025-12-25) — Agent skill for GitHub CLI operations and PR management
+- **Linear MCP Integration Skill**: `.codex/skills/linear-mcp-integration/SKILL.md` (2025-12-25) — Agent skill for Linear MCP functions and issue management
+- **PR Review Integration Skill**: `.codex/skills/pr-review-integration/SKILL.md` (2025-12-25) — Combined patterns for PR review workflows integrating GitHub and Linear (to be evaluated/repurposed)
 - **Research: PR Review Approach**: `.devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_pr-review-approach.md` (2025-12-25) — Research on PR review architecture, workflow vs skill decision, and recommended approach
 - **Research: Skills Review**: `.devagent/workspace/features/completed/2025-12-25_pr-review-agent/research/2025-12-25_skills-review.md` (2025-12-25) — Review of existing skills, assessment of quality and appropriateness, recommendations for workflow integration
 - **Implementation Plan**: `.devagent/workspace/features/completed/2025-12-25_pr-review-agent/plan/2025-12-25_pr-review-agent-plan.md` (2025-12-25) — Complete implementation plan with 5 tasks covering template, workflow, command file, documentation, and testing

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

@@ -135,9 +135,9 @@ Research completed:
 **Dependencies:**
 - GitHub CLI (`gh`) must be installed and authenticated
 - Linear MCP server must be configured and available
-- **GitHub CLI Operations Skill**: `.claude/skills/github-cli-operations/` (✅ Keep - referenced in workflow for PR operations)
-- **Linear MCP Integration Skill**: `.claude/skills/linear-mcp-integration/` (✅ Keep - referenced in workflow for issue operations)
-- **PR Review Integration Skill**: `.claude/skills/pr-review-integration/` (❌ Remove - replaced by this workflow)
+- **GitHub CLI Operations Skill**: `.codex/skills/github-cli-operations/` (✅ Keep - referenced in workflow for PR operations)
+- **Linear MCP Integration Skill**: `.codex/skills/linear-mcp-integration/` (✅ Keep - referenced in workflow for issue operations)
+- **PR Review Integration Skill**: `.codex/skills/pr-review-integration/` (❌ Remove - replaced by this workflow)
 - DevAgent workflow structure and templates
 
 **Technical Considerations:**
@@ -350,9 +350,9 @@ Refer to the AGENTS.md file in the feature directory (`.devagent/workspace/featu
 - Research Workflow: `.devagent/core/workflows/research.md` (workflow structure reference)
 
 **Skills:**
-- GitHub CLI Operations: `.claude/skills/github-cli-operations/SKILL.md` (✅ Keep - referenced in workflow)
-- Linear MCP Integration: `.claude/skills/linear-mcp-integration/SKILL.md` (✅ Keep - referenced in workflow)
-- PR Review Integration: `.claude/skills/pr-review-integration/SKILL.md` (❌ Remove - replaced by workflow)
+- GitHub CLI Operations: `.codex/skills/github-cli-operations/SKILL.md` (✅ Keep - referenced in workflow)
+- Linear MCP Integration: `.codex/skills/linear-mcp-integration/SKILL.md` (✅ Keep - referenced in workflow)
+- PR Review Integration: `.codex/skills/pr-review-integration/SKILL.md` (❌ Remove - replaced by workflow)
 
 **Constitution References:**
 - C3: Delivery Principles (human-in-the-loop, traceable artifacts) — `.devagent/workspace/memory/constitution.md`