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+# AGENTS.md - Complete Guide for Code Agents Working on Agent OS
+
+> **๐ค FOR FUTURE AGENTS:** This is your complete playbook for working on Agent OS. Read this FIRST before making any changes to avoid critical sync issues that have caused problems in the past.
+
+## ๐จ CRITICAL RULE: The Three-Context Problem
+
+**NEVER edit installed files directly!** Always work on source code first.
+
+## ๐ QUICK START FOR NEW AGENTS
+
+If you're an AI agent tasked with working on Agent OS, follow this sequence:
+
+1. **๐ UNDERSTAND THE CONTEXT**: Read this entire file first
+2. **๐งน CHECK WORKSPACE**: Run `./check-agent-os.sh` to verify setup
+3. **๐ START FRESH**: Always create a feature branch for changes
+4. **โ
FOLLOW THE WORKFLOW**: Source โ Commit โ Install โ Test
+5. **๐ VERIFY EVERYTHING**: Use the checklists in this document
+
+### Common Agent Tasks & Quick Commands
+
+| Task | Commands to Run |
+|------|----------------|
+| **Fix a script bug** | 1. Edit `scripts/filename.sh`
2. `./setup.sh --overwrite-instructions`
3. Test: `~/.agent-os/scripts/filename.sh` |
+| **Add new Claude command** | 1. Create `commands/new-command.md`
2. Add to `setup-claude-code.sh`
3. `./setup-claude-code.sh --overwrite-commands` |
+| **Update instruction file** | 1. Edit `instructions/core/filename.md`
2. `./setup.sh --overwrite-instructions`
3. Test: Check `~/.agent-os/instructions/core/` |
+| **Modify installer** | 1. Edit `setup.sh` or `setup-claude-code.sh`
2. Test locally first
3. Verify end-to-end |
+
+## The Three-Context Problem
+
+Agent OS operates in three distinct contexts that can get out of sync:
+
+1. **REPO** (`~/Projects/agent-os/`) - **THIS REPOSITORY** - The source code we work on
+2. **SYSTEM** (`~/.agent-os/`) - Global framework installation on user machines
+3. **PROJECT** (`YourProject/.agent-os/`) - Project-specific configuration
+
+**โ ๏ธ SYNC ISSUE:** Bugs have been fixed in installed versions but not source code, causing future installs to wipe out fixes.
+
+## Installation Flow Mapping
+
+### 1. Base Installation (`setup.sh`)
+
+**Source Location** โ **Installation Destination** โ **Purpose**
+
+#### Standards (User Customizable)
+```bash
+standards/tech-stack.md โ ~/.agent-os/standards/tech-stack.md # Tech stack templates
+standards/code-style.md โ ~/.agent-os/standards/code-style.md # Code style templates
+standards/best-practices.md โ ~/.agent-os/standards/best-practices.md # Best practices templates
+```
+*Note: These preserve user customizations unless `--overwrite-standards` is used*
+
+#### Core Instructions (Always Updated)
+```bash
+instructions/core/analyze-product.md โ ~/.agent-os/instructions/core/analyze-product.md
+instructions/core/create-spec.md โ ~/.agent-os/instructions/core/create-spec.md
+instructions/core/execute-tasks.md โ ~/.agent-os/instructions/core/execute-tasks.md
+instructions/core/execute-task.md โ ~/.agent-os/instructions/core/execute-task.md
+instructions/core/plan-product.md โ ~/.agent-os/instructions/core/plan-product.md
+instructions/meta/pre-flight.md โ ~/.agent-os/instructions/meta/pre-flight.md
+```
+
+#### Scripts (Always Updated)
+```bash
+scripts/workspace-hygiene-check.sh โ ~/.agent-os/scripts/workspace-hygiene-check.sh
+scripts/project-context-loader.sh โ ~/.agent-os/scripts/project-context-loader.sh
+scripts/task-validator.sh โ ~/.agent-os/scripts/task-validator.sh
+scripts/update-documentation.sh โ ~/.agent-os/scripts/update-documentation.sh
+scripts/update-documentation-wrapper.sh โ ~/.agent-os/scripts/update-documentation-wrapper.sh
+scripts/lib/update-documentation-lib.sh โ ~/.agent-os/scripts/lib/update-documentation-lib.sh
+scripts/lib/spec-creator.sh โ ~/.agent-os/scripts/lib/spec-creator.sh
+scripts/lib/roadmap-sync.sh โ ~/.agent-os/scripts/lib/roadmap-sync.sh
+scripts/config-resolver.py โ ~/.agent-os/scripts/config-resolver.py
+scripts/session-memory.sh โ ~/.agent-os/scripts/session-memory.sh
+scripts/config-validator.sh โ ~/.agent-os/scripts/config-validator.sh
+scripts/pre-command-guard.sh โ ~/.agent-os/scripts/pre-command-guard.sh
+scripts/intent-analyzer.sh โ ~/.agent-os/scripts/intent-analyzer.sh
+scripts/workspace-state.sh โ ~/.agent-os/scripts/workspace-state.sh
+scripts/context-aware-wrapper.sh โ ~/.agent-os/scripts/context-aware-wrapper.sh
+scripts/testing-enforcer.sh โ ~/.agent-os/scripts/testing-enforcer.sh
+scripts/workflow-validator.sh โ ~/.agent-os/scripts/workflow-validator.sh
+scripts/work-session-manager.sh โ ~/.agent-os/scripts/work-session-manager.sh
+scripts/commit-boundary-manager.sh โ ~/.agent-os/scripts/commit-boundary-manager.sh
+scripts/session-auto-start.sh โ ~/.agent-os/scripts/session-auto-start.sh
+scripts/check-updates.sh โ ~/.agent-os/scripts/check-updates.sh
+scripts/validate-instructions.sh โ ~/.agent-os/scripts/validate-instructions.sh
+scripts/project_root_resolver.py โ ~/.agent-os/scripts/project_root_resolver.py
+```
+
+#### Workflow Modules (Always Updated)
+```bash
+workflow-modules/step-1-hygiene-and-setup.md โ ~/.agent-os/workflow-modules/step-1-hygiene-and-setup.md
+workflow-modules/step-2-planning-and-execution.md โ ~/.agent-os/workflow-modules/step-2-planning-and-execution.md
+workflow-modules/step-3-quality-assurance.md โ ~/.agent-os/workflow-modules/step-3-quality-assurance.md
+workflow-modules/step-4-git-integration.md โ ~/.agent-os/workflow-modules/step-4-git-integration.md
+```
+
+#### Tools (Always Updated)
+```bash
+tools/aos โ ~/.agent-os/tools/aos # Unified CLI tool
+```
+
+#### Version Tracking
+```bash
+VERSION โ ~/.agent-os/VERSION # Version tracking
+```
+
+### 2. Claude Code Installation (`setup-claude-code.sh`)
+
+**Source Location** โ **Installation Destination** โ **Purpose**
+
+#### Commands (Claude Code Slash Commands)
+```bash
+commands/plan-product.md โ ~/.claude/commands/plan-product.md
+commands/create-spec.md โ ~/.claude/commands/create-spec.md
+commands/execute-tasks.md โ ~/.claude/commands/execute-tasks.md
+commands/analyze-product.md โ ~/.claude/commands/analyze-product.md
+commands/hygiene-check.md โ ~/.claude/commands/hygiene-check.md
+commands/update-documentation.md โ ~/.claude/commands/update-documentation.md
+commands/workflow-status.md โ ~/.claude/commands/workflow-status.md
+commands/workflow-complete.md โ ~/.claude/commands/workflow-complete.md
+```
+
+#### Agent Definitions (Builder Methods Subagents)
+```bash
+claude-code/agents/context-fetcher.md โ ~/.claude/agents/context-fetcher.md
+claude-code/agents/date-checker.md โ ~/.claude/agents/date-checker.md
+claude-code/agents/file-creator.md โ ~/.claude/agents/file-creator.md
+claude-code/agents/git-workflow.md โ ~/.claude/agents/git-workflow.md
+claude-code/agents/test-runner.md โ ~/.claude/agents/test-runner.md
+```
+
+#### Hooks (Workflow Enforcement)
+```bash
+hooks/workflow-enforcement-hook.py โ ~/.agent-os/hooks/workflow-enforcement-hook.py
+hooks/stop-hook.sh โ ~/.agent-os/hooks/stop-hook.sh
+hooks/user-prompt-submit-hook.sh โ ~/.agent-os/hooks/user-prompt-submit-hook.sh
+hooks/pre-bash-hook.sh โ ~/.agent-os/hooks/pre-bash-hook.sh
+hooks/post-bash-hook.sh โ ~/.agent-os/hooks/post-bash-hook.sh
+hooks/task-status-sync.sh โ ~/.agent-os/hooks/task-status-sync.sh
+hooks/notify-hook.sh โ ~/.agent-os/hooks/notify-hook.sh
+hooks/install-hooks.sh โ ~/.agent-os/hooks/install-hooks.sh
+hooks/claude-code-hooks.json โ ~/.agent-os/hooks/claude-code-hooks.json
+
+# Hook utilities
+hooks/lib/workflow-detector.sh โ ~/.agent-os/hooks/lib/workflow-detector.sh
+hooks/lib/git-utils.sh โ ~/.agent-os/hooks/lib/git-utils.sh
+hooks/lib/context-builder.sh โ ~/.agent-os/hooks/lib/context-builder.sh
+hooks/lib/evidence-standards.sh โ ~/.agent-os/hooks/lib/evidence-standards.sh
+hooks/lib/project-config-injector.sh โ ~/.agent-os/hooks/lib/project-config-injector.sh
+hooks/lib/testing-enforcer.sh โ ~/.agent-os/hooks/lib/testing-enforcer.sh
+hooks/lib/testing-reminder.sh โ ~/.agent-os/hooks/lib/testing-reminder.sh
+hooks/lib/workflow-reminder.sh โ ~/.agent-os/hooks/lib/workflow-reminder.sh
+```
+
+### 3. Cursor Installation (`setup-cursor.sh`)
+
+**Source Location** โ **Installation Destination** โ **Purpose**
+
+#### Project-Specific Rules (Created in each project)
+```bash
+commands/plan-product.md โ .cursor/rules/plan-product.mdc # Cursor rule format
+commands/create-spec.md โ .cursor/rules/create-spec.mdc # with front-matter
+commands/execute-tasks.md โ .cursor/rules/execute-tasks.mdc
+commands/analyze-product.md โ .cursor/rules/analyze-product.mdc
+commands/hygiene-check.md โ .cursor/rules/hygiene-check.mdc
+```
+
+## โ ๏ธ CRITICAL GAPS IDENTIFIED
+
+### Files NOT Installed by Any Script
+
+These source files exist but are NOT installed anywhere:
+
+#### Commands Not Installed
+```bash
+commands/work-session.md # โ NOT INSTALLED BY ANY SCRIPT
+```
+
+#### Instructions Not Installed
+```bash
+instructions/core/hygiene-check.md # โ NOT INSTALLED BY setup.sh but should be!
+```
+
+#### Scripts Not Installed
+```bash
+scripts/pre-commit-docs-guard.sh # โ NOT INSTALLED BY ANY SCRIPT
+scripts/verify-installation.sh # โ NOT INSTALLED BY ANY SCRIPT
+scripts/workflow-complete.sh # โ NOT INSTALLED BY ANY SCRIPT
+scripts/workflow-status.sh # โ NOT INSTALLED BY ANY SCRIPT
+```
+
+#### Hook Files Not Installed
+```bash
+hooks/uninstall-hooks.sh # โ NOT INSTALLED BY ANY SCRIPT
+hooks/agent-os-bash-hooks.json # โ NOT INSTALLED BY ANY SCRIPT
+hooks/context_aware_hook.py # โ NOT INSTALLED BY ANY SCRIPT
+hooks/intent_analyzer.py # โ NOT INSTALLED BY ANY SCRIPT
+hooks/bash_command_validator_example.py # โ NOT INSTALLED BY ANY SCRIPT
+```
+
+#### Test Files (Intentionally Not Installed)
+```bash
+hooks/test_*.py # โ Test files - correctly excluded
+hooks/tests/ # โ Test directory - correctly excluded
+```
+
+### Files Installed but Not in Source
+
+These files are downloaded but don't exist in source:
+
+```bash
+# From integrations/setup-subagent-integration.sh (downloaded by setup-claude-code.sh)
+# This may not exist in the repository but is referenced in the installer
+```
+
+## MANDATORY DEVELOPMENT WORKFLOW
+
+### โ ๏ธ THE SYNC PROBLEM
+
+**Problem:** Developers fix bugs in installed files (`~/.agent-os/`, `~/.claude/`) but don't update source code. Future installs wipe out the fixes.
+
+**Solution:** ALWAYS work on source code first, then install.
+
+### โ
CORRECT WORKFLOW
+
+1. **EDIT SOURCE CODE** (in this repository)
+ ```bash
+ # Work on files in:
+ # - commands/
+ # - scripts/
+ # - hooks/
+ # - instructions/
+ # - standards/
+ # - claude-code/agents/
+ ```
+
+2. **COMMIT CHANGES** to repository
+ ```bash
+ git add .
+ git commit -m "Fix: Description of the fix"
+ git push
+ ```
+
+3. **INSTALL FROM SOURCE**
+ ```bash
+ # Install base system from updated source
+ ./setup.sh --overwrite-instructions --overwrite-standards
+
+ # Install Claude Code components from updated source
+ ./setup-claude-code.sh --overwrite-commands
+
+ # Or install from remote repository
+ curl -sSL https://raw.githubusercontent.com/carmandale/agent-os/main/setup.sh | bash -s -- --overwrite-instructions
+ ```
+
+4. **TEST THE INSTALLATION**
+ ```bash
+ # Test the aos CLI
+ aos status
+
+ # Test Claude Code commands
+ # Use /hygiene-check or /plan-product in Claude Code
+
+ # Test scripts directly
+ ~/.agent-os/scripts/workspace-hygiene-check.sh
+ ```
+
+5. **VERIFY CHANGES TOOK EFFECT**
+ ```bash
+ # Compare source and installed files
+ diff scripts/workspace-hygiene-check.sh ~/.agent-os/scripts/workspace-hygiene-check.sh
+
+ # Check installed file timestamps
+ ls -la ~/.agent-os/scripts/workspace-hygiene-check.sh
+ ```
+
+### โ WRONG WORKFLOW (DO NOT DO THIS)
+
+```bash
+# DON'T edit installed files directly
+nano ~/.agent-os/scripts/workspace-hygiene-check.sh # โ WRONG
+nano ~/.claude/commands/plan-product.md # โ WRONG
+
+# DON'T skip source code updates
+# Fix bug in installed file but not source = future installs break # โ WRONG
+```
+
+## VERIFICATION CHECKLIST
+
+Before claiming any fix is complete:
+
+### ๐ Source Code Verification
+- [ ] Changes made to source files in repository
+- [ ] Source code committed and pushed to main branch
+- [ ] Version bumped if needed (in `VERSION` file)
+
+### ๐ Installation Verification
+- [ ] Ran installer script(s) with overwrite flags
+- [ ] Verified installed files match source files
+- [ ] Checked file timestamps to confirm update
+
+### ๐ Functionality Verification
+- [ ] Tested the specific fix in action
+- [ ] Verified no regression in other functionality
+- [ ] Tested via appropriate interface (CLI, Claude Code commands, etc.)
+
+### ๐ Gap Verification
+- [ ] Confirmed fix addresses identified gaps in this document
+- [ ] No orphaned files in source that aren't installed
+- [ ] No references to non-existent files in installers
+
+## INSTALLER MODIFICATION WORKFLOW
+
+When modifying the installers themselves:
+
+1. **Edit installer scripts** in repository root:
+ - `setup.sh` - Base installation
+ - `setup-claude-code.sh` - Claude Code installation
+ - `setup-cursor.sh` - Cursor installation
+
+2. **Test installer locally**:
+ ```bash
+ # Test base installer
+ ./setup.sh --overwrite-instructions --overwrite-standards
+
+ # Test Claude Code installer
+ ./setup-claude-code.sh --overwrite-commands
+ ```
+
+3. **Verify via remote install** (after pushing changes):
+ ```bash
+ # Test remote installation
+ curl -sSL https://raw.githubusercontent.com/carmandale/agent-os/main/setup.sh | bash
+ ```
+
+## DEBUGGING INSTALLATION ISSUES
+
+### Common Issues and Solutions
+
+#### Issue: "File not found" during installation
+**Diagnosis:** Installer references file that doesn't exist in source
+**Solution:**
+1. Check if file exists in source repository
+2. If missing, either create it or remove reference from installer
+3. Update this AGENTS.md document
+
+#### Issue: Changes not taking effect after installation
+**Diagnosis:** Source file not updated or installer not grabbing latest
+**Solution:**
+1. Verify changes exist in source file
+2. Check file is listed in installer script
+3. Run installer with overwrite flags
+4. Check file timestamps in installed location
+
+#### Issue: Installation succeeds but functionality broken
+**Diagnosis:** Dependency missing or file permissions wrong
+**Solution:**
+1. Check all referenced files exist
+2. Verify script permissions (`chmod +x` needed)
+3. Test scripts individually before testing full workflow
+
+## MAINTENANCE NOTES
+
+### When Adding New Files
+
+1. **Add to appropriate installer** (`setup.sh`, `setup-claude-code.sh`, or `setup-cursor.sh`)
+2. **Update this AGENTS.md** mapping section
+3. **Test installation** end-to-end
+4. **Document any new gaps** in the verification checklist
+
+### When Removing Files
+
+1. **Remove from installer scripts**
+2. **Update this AGENTS.md** mapping section
+3. **Consider migration/cleanup** for existing installations
+4. **Test that removal doesn't break** dependent functionality
+
+### Version Management
+
+- **Source of truth:** `VERSION` file in repository root
+- **Installed version:** `~/.agent-os/VERSION` (copied from source)
+- **Update process:** Increment version in source, commit, then install
+
+## ๐ค AGENT-SPECIFIC GUIDANCE
+
+### AI Agent Safety Guards
+
+**๐จ BEFORE MAKING ANY CHANGES:**
+
+1. **Read the entire AGENTS.md file** (this file) - don't skip sections
+2. **Check existing issues and PRs** to avoid duplicate work
+3. **Verify you understand the three-context problem**
+4. **Always test your changes** before claiming completion
+
+### Common Agent Mistakes to Avoid
+
+โ **DON'T:** Edit files in `~/.agent-os/` or `~/.claude/` directly
+โ
**DO:** Edit source files in the repository, then install
+
+โ **DON'T:** Assume installation worked without testing
+โ
**DO:** Run verification commands after installation
+
+โ **DON'T:** Mix multiple unrelated changes in one commit
+โ
**DO:** Create focused commits for specific fixes
+
+โ **DON'T:** Skip the feature branch workflow
+โ
**DO:** Always work on feature branches, never commit directly to main
+
+### Testing Patterns for Common Changes
+
+#### When Modifying Scripts
+```bash
+# 1. Edit source file
+nano scripts/workspace-hygiene-check.sh
+
+# 2. Install with overwrite
+./setup.sh --overwrite-instructions
+
+# 3. Test directly
+~/.agent-os/scripts/workspace-hygiene-check.sh
+
+# 4. Verify it matches source
+diff scripts/workspace-hygiene-check.sh ~/.agent-os/scripts/workspace-hygiene-check.sh
+```
+
+#### When Adding Claude Commands
+```bash
+# 1. Create source file
+nano commands/new-command.md
+
+# 2. Add to installer
+nano setup-claude-code.sh # Add to the commands loop
+
+# 3. Install with overwrite
+./setup-claude-code.sh --overwrite-commands
+
+# 4. Verify installation
+ls -la ~/.claude/commands/new-command.md
+```
+
+#### When Fixing Installer Issues
+```bash
+# 1. Edit installer
+nano setup.sh
+
+# 2. Test locally
+./setup.sh --overwrite-instructions --overwrite-standards
+
+# 3. Check status
+aos status
+
+# 4. Test remote install (after pushing)
+curl -sSL https://raw.githubusercontent.com/carmandale/agent-os/main/setup.sh | bash
+```
+
+### Quality Assurance Commands
+
+Always run these before claiming work is complete:
+
+```bash
+# Syntax validation
+bash -n setup.sh
+bash -n setup-claude-code.sh
+bash -n setup-cursor.sh
+
+# Installation test
+./check-agent-os.sh
+
+# Status verification
+~/.agent-os/tools/aos status
+
+# File comparison (for changed files)
+diff scripts/filename.sh ~/.agent-os/scripts/filename.sh
+```
+
+### Emergency Recovery
+
+If you accidentally edit installed files instead of source:
+
+```bash
+# 1. STOP - don't commit anything yet
+# 2. Copy your changes to the source files manually
+# 3. Reinstall from source to verify
+./setup.sh --overwrite-instructions --overwrite-standards
+# 4. Test that your changes work
+# 5. Then commit the source changes
+```
+
+### Agent Success Checklist
+
+Before completing any task:
+
+- [ ] **Understanding**: I read this AGENTS.md file completely
+- [ ] **Source First**: I edited source files, not installed files
+- [ ] **Installation**: I ran the appropriate installer with overwrite flags
+- [ ] **Testing**: I verified the changes work as expected
+- [ ] **Verification**: I compared source and installed files to ensure sync
+- [ ] **Quality**: I ran syntax checks and status commands
+- [ ] **Documentation**: I updated relevant docs if needed
+- [ ] **Branch**: I worked on a feature branch, not main
+- [ ] **Commit**: I made focused commits with clear messages
+
+### Quick Reference Commands
+
+```bash
+# Check overall status
+./check-agent-os.sh
+~/.agent-os/tools/aos status
+
+# Reinstall everything
+./setup.sh --overwrite-instructions --overwrite-standards
+./setup-claude-code.sh --overwrite-commands
+
+# Verify file sync
+diff commands/plan-product.md ~/.claude/commands/plan-product.md
+diff scripts/workspace-hygiene-check.sh ~/.agent-os/scripts/workspace-hygiene-check.sh
+
+# Syntax checks
+bash -n setup.sh
+bash -n setup-claude-code.sh
+
+# Create feature branch
+git checkout -b feature/your-change-description
+```
+
+## ๐ METRICS FOR AGENTS
+
+Track these to ensure quality:
+
+- **Files Changed**: List all source files modified
+- **Installation Commands Run**: Document which installers were executed
+- **Tests Passed**: Show output of verification commands
+- **Sync Verified**: Prove source and installed files match
+- **Quality Checks**: Show syntax validation results
+
+### Evidence Template for Agent Work
+
+```markdown
+## Evidence/Test Results/Verification
+
+### Files Modified
+- scripts/workspace-hygiene-check.sh (fixed bug in line 42)
+- commands/new-feature.md (added new command)
+
+### Installation Process
+```bash
+$ ./setup.sh --overwrite-instructions
+โ
Script installed successfully
+
+$ ./setup-claude-code.sh --overwrite-commands
+โ
Commands installed successfully
+```
+
+### Verification Results
+```bash
+$ diff scripts/workspace-hygiene-check.sh ~/.agent-os/scripts/workspace-hygiene-check.sh
+# No output = files match โ
+
+$ ~/.agent-os/scripts/workspace-hygiene-check.sh
+โ
Script executes successfully
+
+$ aos status
+โ
All components current
+```
+
+### Quality Assurance
+```bash
+$ bash -n setup.sh
+โ
Syntax valid
+
+$ ./check-agent-os.sh
+๐ Agent OS is ready to use!
+```
+```
+
+---
+
+**Last Updated:** 2025-01-27
+**Document Version:** 2.0.0 - Enhanced for AI Agents
+**Next Review:** When source-to-installation mappings change
+
+*๐ค This document is specifically designed for AI agents working on Agent OS. Follow it religiously to avoid sync issues.*
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