refactor(claude): upgrade slash commands to md files

Latest way of doing slash commands for claude is to use markdown
files under .claude/commands. YOu can namespace them, and doing this
gets you integration with the /help command and the ability to
run bash using the ! marker.

Author: RickCogley

claude/.claude/CLAUDE.md

@@ -0,0 +1,52 @@
+[
+  {
+    "name": "memin",
+    "description": "Load global and project memory files",
+    "prompt": "Read the following memory files in order:\n1. Global memory at ~/.claude/CLAUDE.md\n2. Project memory at @CLAUDE.md (if it exists)\n\nSummarize what you've learned from these files, particularly any rules about git commits, PR descriptions, and coding standards."
+  },
+  {
+    "name": "security-rules",
+    "description": "Show DevSkim and CodeQL suppression syntax",
+    "prompt": "Show me the security scanning suppression syntax rules from the global memory, specifically the DevSkim and CodeQL sections. Focus on the correct placement and syntax for each tool."
+  },
+  {
+    "name": "preflight",
+    "description": "Show preflight checks for current project",
+    "prompt": "Based on the project type (check for deno.json, package.json, pyproject.toml, etc.), show me the appropriate preflight checks I should run before committing code."
+  },
+  {
+    "name": "owasp",
+    "description": "Show OWASP Top 10 security checklist",
+    "prompt": "Show me the OWASP Top 10 checklist from global memory. Display each item with its title and key verification points."
+  },
+  {
+    "name": "commit-style",
+    "description": "Show conventional commit format and InfoSec guidelines",
+    "prompt": "Show me the conventional commit format and InfoSec guidelines from global memory. Include examples of when to use InfoSec comments and the proper format."
+  },
+  {
+    "name": "directory-structure",
+    "description": "Show recommended project directory structure",
+    "prompt": "Show me the recommended project directory structure from global memory. Include the standard directories, their purposes, and examples for different languages."
+  },
+  {
+    "name": "checkpoint",
+    "description": "Save session summary to docs/checkpoints/checkpoint-YYYY-MM-DD-{descriptive-name}.md",
+    "prompt": "Create a session checkpoint by following these steps in order:\n\n1. CREATE CHECKPOINT FILE:\n   - Path: `docs/checkpoints/checkpoint-YYYY-MM-DD-{descriptive-name}.md` (use today's date and a descriptive name based on the work done)\n   - Create directory if needed: `mkdir -p docs/checkpoints`\n   - Use markdown format\n\n2. CHECKPOINT CONTENT (use these exact sections):\n   # Session Checkpoint - YYYY-MM-DD - {Descriptive Name}\n   \n   ## Summary of Work Accomplished\n   List main tasks completed with brief descriptions\n   \n   ## Key Technical Decisions\n   Document important architectural/implementation choices and rationale\n   \n   ## Files Created/Modified\n   ### Created\n   - List new files with purpose\n   ### Modified\n   - List changed files with type of change\n   \n   ## Problems Solved\n   List issues resolved and their solutions\n   \n   ## Lessons Learned\n   Key insights or patterns discovered\n   \n   ## Next Steps\n   Potential future work or improvements\n\nIf a checkpoint for today already exists with the same descriptive name, append to it with a timestamp separator. Show progress after each step. If any step fails, report the error and continue with remaining steps."
+  },
+  {
+    "name": "project",
+    "description": "Manage project-specific memory",
+    "prompt": "Manage project-specific memory files. Use the following commands:\n- `/project add <file>`: Add a file to the project context\n- `/project remove <file>`: Remove a file from the project context\n- `/project list`: List all files in the project context"
+  },
+  {
+    "name": "commands",
+    "description": "List all available slash commands",
+    "prompt": "List all available slash commands from ~/.claude/settings.json in a clear, formatted way. You can use jq to do this. Include the command name, description, and prompt for each command."
+  },
+  {
+    "name": "addglobal",
+    "description": "Add global config to project context",
+    "prompt": "/project add ~/.claude/CLAUDE.md"
+  }
+]

claude/.claude/commands/BACKUP-slash-commands-20250714-214851.json

@@ -0,0 +1,52 @@
+[
+  {
+    "name": "memin",
+    "description": "Load global and project memory files",
+    "prompt": "Read the following memory files in order:\n1. Global memory at ~/.claude/CLAUDE.md\n2. Project memory at @CLAUDE.md (if it exists)\n\nSummarize what you've learned from these files, particularly any rules about git commits, PR descriptions, and coding standards."
+  },
+  {
+    "name": "security-rules",
+    "description": "Show DevSkim and CodeQL suppression syntax",
+    "prompt": "Show me the security scanning suppression syntax rules from the global memory, specifically the DevSkim and CodeQL sections. Focus on the correct placement and syntax for each tool."
+  },
+  {
+    "name": "preflight",
+    "description": "Show preflight checks for current project",
+    "prompt": "Based on the project type (check for deno.json, package.json, pyproject.toml, etc.), show me the appropriate preflight checks I should run before committing code."
+  },
+  {
+    "name": "owasp",
+    "description": "Show OWASP Top 10 security checklist",
+    "prompt": "Show me the OWASP Top 10 checklist from global memory. Display each item with its title and key verification points."
+  },
+  {
+    "name": "commit-style",
+    "description": "Show conventional commit format and InfoSec guidelines",
+    "prompt": "Show me the conventional commit format and InfoSec guidelines from global memory. Include examples of when to use InfoSec comments and the proper format."
+  },
+  {
+    "name": "directory-structure",
+    "description": "Show recommended project directory structure",
+    "prompt": "Show me the recommended project directory structure from global memory. Include the standard directories, their purposes, and examples for different languages."
+  },
+  {
+    "name": "checkpoint",
+    "description": "Save session summary to docs/checkpoints/checkpoint-YYYY-MM-DD-{descriptive-name}.md",
+    "prompt": "Create a session checkpoint by following these steps in order:\n\n1. CREATE CHECKPOINT FILE:\n   - Path: `docs/checkpoints/checkpoint-YYYY-MM-DD-{descriptive-name}.md` (use today's date and a descriptive name based on the work done)\n   - Create directory if needed: `mkdir -p docs/checkpoints`\n   - Use markdown format\n\n2. CHECKPOINT CONTENT (use these exact sections):\n   # Session Checkpoint - YYYY-MM-DD - {Descriptive Name}\n   \n   ## Summary of Work Accomplished\n   List main tasks completed with brief descriptions\n   \n   ## Key Technical Decisions\n   Document important architectural/implementation choices and rationale\n   \n   ## Files Created/Modified\n   ### Created\n   - List new files with purpose\n   ### Modified\n   - List changed files with type of change\n   \n   ## Problems Solved\n   List issues resolved and their solutions\n   \n   ## Lessons Learned\n   Key insights or patterns discovered\n   \n   ## Next Steps\n   Potential future work or improvements\n\nIf a checkpoint for today already exists with the same descriptive name, append to it with a timestamp separator. Show progress after each step. If any step fails, report the error and continue with remaining steps."
+  },
+  {
+    "name": "project",
+    "description": "Manage project-specific memory",
+    "prompt": "Manage project-specific memory files. Use the following commands:\n- `/project add <file>`: Add a file to the project context\n- `/project remove <file>`: Remove a file from the project context\n- `/project list`: List all files in the project context"
+  },
+  {
+    "name": "commands",
+    "description": "List all available slash commands",
+    "prompt": "List all available slash commands from ~/.claude/settings.json in a clear, formatted way. You can use jq to do this. Include the command name, description, and prompt for each command."
+  },
+  {
+    "name": "addglobal",
+    "description": "Add global config to project context",
+    "prompt": "/project add ~/.claude/CLAUDE.md"
+  }
+]

claude/.claude/commands/BACKUP-slash-commands.json

@@ -0,0 +1,126 @@
+# Claude Commands Migration Summary
+
+## Migration Details
+- **Date**: 2025-07-14
+- **Migration Type**: Legacy commands to MCP (Model Context Protocol) format
+- **Backup Location**: Original commands preserved with `.bak` extension
+
+## Commands Migrated
+
+The following 10 commands were successfully migrated to the new MCP format:
+
+1. **analyze-project** → `mcp__aichaku-reviewer__analyze_project`
+   - Analyzes project structure, languages, architecture, and dependencies
+   
+2. **create-doc-template** → `mcp__aichaku-reviewer__create_doc_template`
+   - Creates documentation template files for tutorials, how-tos, references, etc.
+   
+3. **generate-documentation** → `mcp__aichaku-reviewer__generate_documentation`
+   - Generates comprehensive documentation following selected standards
+   
+4. **get-standards** → `mcp__aichaku-reviewer__get_standards`
+   - Gets currently selected standards for the project
+   
+5. **get-statistics** → `mcp__aichaku-reviewer__get_statistics`
+   - Gets usage statistics and analytics for MCP tool usage
+   
+6. **repo-list** → `mcp__github-operations__repo_list`
+   - Lists user repositories
+   
+7. **review-file** → `mcp__aichaku-reviewer__review_file`
+   - Reviews a file for security, standards, and methodology compliance
+   
+8. **review-methodology** → `mcp__aichaku-reviewer__review_methodology`
+   - Checks if project follows selected methodology patterns
+   
+9. **run-list** → `mcp__github-operations__run_list`
+   - Lists GitHub Actions workflow runs
+   
+10. **run-view** → `mcp__github-operations__run_view`
+    - Views GitHub Actions workflow run details
+
+## Benefits of the New MCP Format
+
+### 1. **Standardized Protocol**
+- MCP provides a consistent interface for all tools
+- Better integration with Claude's capabilities
+- Improved error handling and validation
+
+### 2. **Enhanced Type Safety**
+- Proper parameter validation
+- Clear type definitions for inputs and outputs
+- Better error messages
+
+### 3. **Automatic Discovery**
+- Tools are automatically discovered by Claude
+- No manual registration required
+- Seamless updates when new tools are added
+
+### 4. **Better Documentation**
+- Each tool has built-in description
+- Parameter documentation included
+- Examples and usage patterns
+
+### 5. **Server-Based Architecture**
+- Tools run as separate MCP servers
+- Better isolation and security
+- Can be updated independently
+
+## How to Use the New Commands
+
+The new MCP commands are automatically available in Claude. Simply use them by their new names:
+
+### Examples:
+
+**Analyze a project:**
+```
+Use mcp__aichaku-reviewer__analyze_project with projectPath: "/path/to/project"
+```
+
+**Review a file:**
+```
+Use mcp__aichaku-reviewer__review_file with file: "/path/to/file.ts"
+```
+
+**List repositories:**
+```
+Use mcp__github-operations__repo_list
+```
+
+**Generate documentation:**
+```
+Use mcp__aichaku-reviewer__generate_documentation with projectPath: "/path/to/project"
+```
+
+### Key Differences:
+1. Commands now use the `mcp__` prefix
+2. Server name is included (e.g., `aichaku-reviewer`, `github-operations`)
+3. Parameters are passed as named arguments
+4. No need to manually load or configure commands
+
+## Legacy Command Backups
+
+All original command files have been preserved with a `.bak` extension in case you need to reference them:
+- `analyze-project.md.bak`
+- `create-doc-template.md.bak`
+- `generate-documentation.md.bak`
+- etc.
+
+These backups are located in the same `~/.claude/commands/` directory.
+
+## Next Steps
+
+1. The new MCP commands are immediately available for use
+2. No action required - Claude will automatically use the new format
+3. Legacy backups can be safely deleted once you're comfortable with the new system
+4. Check MCP server logs at `~/.claude/logs/` if you encounter any issues
+
+## Additional Resources
+
+- MCP Documentation: Available in your Claude settings
+- Server Configuration: `~/.claude/mcp-settings.json`
+- Logs: `~/.claude/logs/mcp-*.log`
+
+---
+
+*This migration was performed automatically to improve the command system's reliability and features.*

claude/.claude/commands/MIGRATION-SUMMARY.md

@@ -0,0 +1,47 @@
+---
+allowed-tools: Write, Bash
+description: Save session summary to docs/checkpoints/checkpoint-YYYY-MM-DD-{descriptive-name}.md
+---
+
+## Context
+- Current date: !`date +%Y-%m-%d`
+- Current time: !`date +%H%M%S`
+- Current directory: !`pwd`
+- Git status: !`git status --porcelain | head -10`
+
+## Your task
+Create a session checkpoint documenting our work. Use the arguments "$ARGUMENTS" as the descriptive name.
+
+Create the checkpoint file at `docs/checkpoints/checkpoint-{current-date}-{descriptive-name}.md` with the following structure:
+
+```markdown
+# Session Checkpoint - {current-date} - {Descriptive Name}
+
+## Summary of Work Accomplished
+[List main tasks completed with brief descriptions]
+
+## Key Technical Decisions  
+[Document important architectural/implementation choices and rationale]
+
+## Files Created/Modified
+
+### Created
+- [List new files with purpose]
+
+### Modified
+- [List changed files with type of change]
+
+## Problems Solved
+[List issues resolved and their solutions]
+
+## Lessons Learned
+[Key insights or patterns discovered]
+
+## Next Steps
+[Potential future work or improvements]
+
+---
+*Checkpoint created: {timestamp}*
+```
+
+First create the docs/checkpoints directory if it doesn't exist, then create the checkpoint file with today's date and the descriptive name from the arguments.

claude/.claude/commands/aichaku/checkpoint.md

@@ -0,0 +1,28 @@
+---
+allowed-tools: Read
+description: Load global and project memory files
+---
+
+# Load Memory Files
+
+I'll load and analyze the relevant memory files for this session.
+
+## 1. Global Memory
+Loading the global memory file that applies to all projects:
+
+@~/.claude/CLAUDE.md
+
+## 2. Project Memory  
+Checking for project-specific memory:
+
+@CLAUDE.md
+
+## Summary
+
+Based on the memory files loaded, I'll summarize what I've learned, particularly:
+- Rules about git commits and PR descriptions
+- Coding standards and conventions
+- Security requirements (OWASP, InfoSec)
+- Project-specific guidelines
+
+$ARGUMENTS

claude/.claude/commands/aichaku/memin.md

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+---
+allowed-tools: Read, Write, Edit, LS
+description: Manage project-specific memory  
+---
+
+## Context
+
+Arguments provided: $ARGUMENTS
+
+Project memory context file: !`echo ~/.claude/project-context.md`
+Current working directory: !`pwd`
+
+## Your task
+
+You are managing project-specific memory files. Parse the subcommand from the arguments and execute the appropriate action:
+
+### If arguments contain "add":
+1. Extract the file path from the arguments (everything after "add")
+2. Validate the file path exists using the Read tool
+3. Add the file path to ~/.claude/project-context.md (create if it doesn't exist)
+4. Confirm the file was added to project context
+
+### If arguments contain "remove":
+1. Extract the file path from the arguments (everything after "remove")
+2. Remove the file path from ~/.claude/project-context.md
+3. Confirm the file was removed from project context
+
+### If arguments contain "list":
+1. Read ~/.claude/project-context.md if it exists
+2. Display all files currently in the project context
+3. If no context file exists, inform that no files are tracked
+
+### Format for ~/.claude/project-context.md:
+```
+# Project Context Files
+
+## Currently Tracked Files
+- /path/to/file1.md
+- /path/to/file2.md
+- /path/to/file3.md
+
+Last updated: [timestamp]
+```
+
+Execute the appropriate action based on the subcommand in the arguments.