Organize Agent Docs

Organize Agent Documentation

Reorganize project agentic documentation to separate universal project information from agent-specific tooling and workflows.

When to Use This Skill

Use this skill when:

• A project has grown to include multiple AI agents (Claude, Gemini, Cursor, Copilot, etc.)
• AGENTS.md or CLAUDE.md contains both universal project info and agent-specific tooling
• You need to add a new agent to an existing project
• Agent documentation has become difficult to maintain due to duplication
• User asks to "organize agent docs", "separate agent instructions", or similar

What This Skill Does

Restructures agentic documentation following a clear separation of concerns pattern:

1. AGENTS.md - Universal project documentation (primary source of truth)

   • Product overview and user persona
   • Recent changes and version history
   • Architecture notes and testing requirements
   • Common agent tasks and workflows
   • Universal critical rules (applies to all agents)

2. CLAUDE.md - Claude-specific instructions

   • MCP server configuration (XcodeBuildMCP, App Store Connect MCP, etc.)
   • Claude-specific build preferences and tooling
   • References to global ~/.claude/CLAUDE.md patterns
   • Claude-specific critical rules

3. GEMINI.md - Gemini-specific instructions

   • Gemini Code Assist integration patterns
   • Standard CLI tool alternatives (for agents without MCP)
   • Gemini API integration notes (if applicable)

4. Additional agent files (as needed)

   • CURSOR.md, COPILOT.md, CODEX.md, etc.

Benefits

✅ Clear separation of concerns - Universal vs. agent-specific content ✅ Single source of truth - AGENTS.md remains primary reference ✅ Scalable - Easy to add new agents without modifying universal docs ✅ No duplication - Agent files reference AGENTS.md, don't duplicate content ✅ Maintainable - Update universal rules once, agent-specific rules independently ✅ Discoverable - Clear structure helps agents find relevant instructions quickly

Prerequisites

The project should have:

• Existing AGENTS.md or CLAUDE.md with agentic instructions
• Content that mixes universal project info with agent-specific tooling
• Multiple AI agents working on the project (or planning to add more)

Usage

Step 1: Analyze Current Documentation

Read the existing agentic documentation to understand what content exists:

# Read primary agent documentation
cat AGENTS.md  # or CLAUDE.md, whichever exists
cat GEMINI.md  # if exists

Identify content types:

• Universal: Product overview, architecture, testing, workflows, general rules
• Claude-specific: MCP servers, Claude tool preferences, Claude-only workflows
• Gemini-specific: Gemini APIs, Gemini-specific patterns
• Other agents: Cursor, Copilot, custom agents

Step 2: Create AGENTS.md (Universal Documentation)

If AGENTS.md doesn't exist, create it. Otherwise, clean it to remove agent-specific content.

Universal content to include:

• Product overview and target user persona
• Recent changes and version history (applies to all agents)
• CLI documentation and automation workflows
• Architecture notes and design patterns
• Testing requirements (unit tests, integration tests, UI tests)
• Common agent tasks (adding tests, fixing bugs, updating docs)
• Universal critical rules (git workflow, version management, testing)

Content to EXCLUDE from AGENTS.md:

• MCP server documentation (move to CLAUDE.md)
• Claude-specific tool preferences (move to CLAUDE.md)
• Agent-specific API integrations (move to respective agent files)

Structure:

# ProjectName - AI Agent Instructions

**Version**: X
**Purpose**: Guide AI agents working on ProjectName
**Audience**: Claude Code, Gemini, and other AI development assistants

## Product Overview
[Product description, target user, core value]

## Recent Changes
[Last 3-5 sprints with what changed, files modified, impact]

## Scripting and Automation
[CLI tools, AppleScript, hooks, CI/CD - universal patterns]

## User Persona Summary
[Primary user, pain points, use cases, design principles]

## Architecture Notes
[Dual interface, platform strategy, testing requirements]

## Documentation Index
[Links to user-facing docs, technical docs, architecture]

## Common Agent Tasks
[Adding tests, fixing bugs, CLI changes, documentation updates]

## Critical Rules for AI Agents
[Universal rules that apply to ALL agents]

1. NEVER commit directly to `main`
2. ALWAYS test both platforms before committing
3. NEVER manually edit version numbers
4. ALWAYS read files before editing
5. NEVER create files unless necessary
6. Follow agent-specific instructions (see CLAUDE.md, GEMINI.md)

Step 3: Create CLAUDE.md (Claude-Specific)

Extract Claude-specific content and create CLAUDE.md:

Claude-specific content:

• MCP server configuration (XcodeBuildMCP, App Store Connect MCP, etc.)
• Build tool preferences (xcodebuild over swift build, etc.)
• Claude-specific critical rules
• References to global ~/.claude/CLAUDE.md settings

Structure:

# Claude-Specific Agent Instructions

**⚠️ Read [AGENTS.md](AGENTS.md) first** for universal project documentation.

This file contains instructions specific to Claude Code agents.

## Claude-Specific Build Preferences
[Tool preferences like xcodebuild over swift build]

## MCP Server Configuration
[XcodeBuildMCP, App Store Connect MCP, custom MCP servers]

### XcodeBuildMCP
**Available Operations**: build_sim, test_sim, etc.
**Usage Pattern**: [Examples]
**Benefits**: [Why use MCP over direct commands]

### App Store Connect MCP
**Available Operations**: list_apps, get_metrics, etc.
**Usage Pattern**: [Examples]

## Claude-Specific Critical Rules
1. ALWAYS use XcodeBuildMCP tools
2. NEVER use swift build/test
3. Leverage MCP servers for automation
4. Follow global CLAUDE.md patterns

## Global Claude Settings
Your global Claude instructions: ~/.claude/CLAUDE.md
Key patterns: [Communication, Security, CI/CD, etc.]

Step 4: Create GEMINI.md (Gemini-Specific)

Create GEMINI.md for Gemini-specific patterns:

Structure:

# Gemini-Specific Agent Instructions

**⚠️ Read [AGENTS.md](AGENTS.md) first** for universal project documentation.

This file contains instructions specific to Google Gemini agents.

## Gemini-Specific Configuration
[Currently configured tools and workflows]

## Gemini-Specific Critical Rules
1. Use standard CLI tools (no MCP access)
2. Follow Xcode best practices
3. Test commands: [Standard xcodebuild commands]

## Future Gemini Integrations
[Placeholder for Gemini API, Code Assist, etc.]

Step 5: Update Cross-References

Update AGENTS.md to reference agent-specific docs:

In automation section:

### 6. Agent-Specific Tools
**Platform**: Varies by agent
**Best For**: Agent-specific automation and integrations

See agent-specific documentation:
- **Claude Code**: [CLAUDE.md](CLAUDE.md) - XcodeBuildMCP, App Store Connect MCP
- **Gemini**: [GEMINI.md](GEMINI.md) - Standard CLI tools

In critical rules:

9. **Follow agent-specific instructions** - See [CLAUDE.md](CLAUDE.md) or [GEMINI.md](GEMINI.md)

Step 6: Verify Organization

Check that the reorganization is complete:

# Verify all files exist
ls -la AGENTS.md CLAUDE.md GEMINI.md

# Check that AGENTS.md has no agent-specific content
grep -i "mcp" AGENTS.md  # Should only appear in cross-references
grep -i "xcodebuild" AGENTS.md  # Should only appear in universal testing docs

# Check that CLAUDE.md references AGENTS.md
head -5 CLAUDE.md  # Should have "Read AGENTS.md first" warning

# Check that GEMINI.md references AGENTS.md
head -5 GEMINI.md  # Should have "Read AGENTS.md first" warning

Step 7: Commit Changes

Commit the reorganized documentation:

git add AGENTS.md CLAUDE.md GEMINI.md
git commit -m "docs: Reorganize agentic instructions into agent-specific files

Separated universal project documentation from agent-specific tooling:

- AGENTS.md: Primary source of truth for universal project info
- CLAUDE.md: Claude-specific instructions (MCP servers, build preferences)
- GEMINI.md: Gemini-specific instructions (standard CLI tools)

Benefits:
- Clear separation of concerns (universal vs. agent-specific)
- Single source of truth with agent-specific extensions
- Scalable for adding new AI agents
- No duplication; agent files reference AGENTS.md"

git push origin development

Content Categorization Guide

Universal Content (AGENTS.md)

Always universal:

• Product overview and mission
• Target user persona and pain points
• Architecture patterns and design decisions
• Testing requirements (applies to all agents)
• Git workflow and branching strategy
• Version management and release process
• Documentation index and structure
• Common agent tasks (bug fixes, testing, docs)

Critical rules (universal):

• NEVER commit to main directly
• NEVER delete development branch
• ALWAYS test both platforms (if multiplatform)
• NEVER manually edit version numbers
• ALWAYS read files before editing
• NEVER create unnecessary files

Claude-Specific Content (CLAUDE.md)

Claude-only:

• MCP server configuration and usage
• XcodeBuildMCP tool operations
• App Store Connect MCP operations
• Custom MCP servers specific to project
• Build tool preferences (when Claude-specific)
• References to global ~/.claude/CLAUDE.md

Critical rules (Claude-specific):

• ALWAYS use XcodeBuildMCP tools
• NEVER use swift build/test (if using XcodeBuildMCP)
• Leverage MCP servers for automation
• Follow global CLAUDE.md communication patterns

Gemini-Specific Content (GEMINI.md)

Gemini-only:

• Gemini API integration patterns
• Gemini Code Assist workflows
• Standard CLI alternatives to MCP tools
• Gemini-specific build commands

Critical rules (Gemini-specific):

• Use standard CLI tools (no MCP access)
• Follow Xcode standard workflows
• Use direct xcodebuild commands

Examples from Real Projects

Example 1: Produciesta (Media Production App)

Before reorganization:

• AGENTS.md: 643 lines mixing universal and Claude-specific content
• CLAUDE.md: 27 lines redirecting to AGENTS.md
• GEMINI.md: 27 lines redirecting to AGENTS.md

After reorganization:

• AGENTS.md: 637 lines of universal content (product, CLI, architecture, testing)
• CLAUDE.md: 135 lines (MCP servers, build preferences, Claude rules)
• GEMINI.md: 44 lines (standard tools, future integrations)

Extracted from AGENTS.md to CLAUDE.md:

• Section 6: XcodeBuildMCP Tools (Development Automation)
• Critical Rule #5: ALWAYS use XcodeBuildMCP tools
• Critical Rule #6: NEVER use swift build/test

Replaced in AGENTS.md:

• Section 6 now points to agent-specific docs
• Critical rules reduced from 10 to 9 universal rules
• Added new rule: "Follow agent-specific instructions"

Example 2: Swift Library Project

AGENTS.md (universal):

• Library architecture and API design
• Testing requirements (SPM tests)
• Documentation generation (DocC)
• Release process (git tags, GitHub releases)

CLAUDE.md (Claude-specific):

• XcodeBuildMCP for swift_package_test
• App Store Connect MCP for TestFlight distribution (if applicable)
• Build preferences (xcodebuild over swift build)

GEMINI.md (Gemini-specific):

• Standard swift test commands
• GitHub Actions workflow patterns
• DocC generation with standard tools

Troubleshooting

Circular References

Problem: AGENTS.md and CLAUDE.md both reference each other, creating confusion.

Solution: Always start with AGENTS.md (universal), then extend with agent-specific files:

• AGENTS.md: Does NOT read other files first (it's the foundation)
• CLAUDE.md: MUST start with "Read AGENTS.md first"
• GEMINI.md: MUST start with "Read AGENTS.md first"

Duplication Between Files

Problem: Same content appears in both AGENTS.md and CLAUDE.md.

Solution: Apply the "single source of truth" principle:

• If it's universal → AGENTS.md only
• If it's Claude-specific → CLAUDE.md only, reference AGENTS.md for context
• Never duplicate; always reference

Agent Can't Find Instructions

Problem: Agent reads CLAUDE.md but misses universal content in AGENTS.md.

Solution: Make the cross-reference explicit and prominent:

• Start CLAUDE.md with: "⚠️ Read AGENTS.md first"
• Add a summary of what's in AGENTS.md
• Include direct links to relevant AGENTS.md sections

Too Many Agent Files

Problem: Project has 5+ agent-specific files, getting hard to maintain.

Solution: Only create agent files when there's substantial agent-specific content:

• If agent only needs 10 lines → Add a section to AGENTS.md instead
• If agent needs 50+ lines → Create dedicated file
• Consider merging rarely-used agent files

Best Practices

1. Start with AGENTS.md - Always establish universal documentation first
2. Agent files are extensions - They add to AGENTS.md, not replace it
3. One source of truth - Never duplicate content across files
4. Explicit cross-references - Make dependencies clear ("Read X first")
5. Update dates - Keep "Last Updated" timestamps current
6. Test organization - Verify agents can find instructions easily
7. Review periodically - Reorganize if universal content ends up in agent files
8. Scale intentionally - Only add agent files when needed, not preemptively

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Notes

• This skill focuses on documentation organization, not content creation
• Assumes project already has some form of agentic documentation
• Works best for projects with 2+ AI agents or planning to scale
• Can be adapted for non-AI documentation (API docs, internal wikis)
• The pattern is based on real-world experience reorganizing Produciesta docs