Reorganized project structure for better maintainability and reduced disk usage by 95.9% (11 GB -> 451 MB). Directory Reorganization (85% reduction in root files): - Created docs/ with subdirectories (deployment, testing, database, etc.) - Created infrastructure/vpn-configs/ for VPN scripts - Moved 90+ files from root to organized locations - Archived obsolete documentation (context system, offline mode, zombie debugging) - Moved all test files to tests/ directory - Root directory: 119 files -> 18 files Disk Cleanup (10.55 GB recovered): - Deleted Rust build artifacts: 9.6 GB (target/ directories) - Deleted Python virtual environments: 161 MB (venv/ directories) - Deleted Python cache: 50 KB (__pycache__/) New Structure: - docs/ - All documentation organized by category - docs/archives/ - Obsolete but preserved documentation - infrastructure/ - VPN configs and SSH setup - tests/ - All test files consolidated - logs/ - Ready for future logs Benefits: - Cleaner root directory (18 vs 119 files) - Logical organization of documentation - 95.9% disk space reduction - Faster navigation and discovery - Better portability (build artifacts excluded) Build artifacts can be regenerated: - Rust: cargo build --release (5-15 min per project) - Python: pip install -r requirements.txt (2-3 min) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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MCP Server Installation Test Results
Test Date: 2026-01-17 Test Environment: Windows (ClaudeTools Project) Node.js Version: v24.11.0
Installation Summary
Status: SUCCESS
All three Phase 1 MCP servers have been successfully installed and configured:
- GitHub MCP Server - Configured (requires token)
- Filesystem MCP Server - Configured and ready
- Sequential Thinking MCP Server - Configured and ready
Package Verification Tests
Test 1: Sequential Thinking MCP Server
Package: @modelcontextprotocol/server-sequential-thinking
Test Command:
npx -y @modelcontextprotocol/server-sequential-thinking
Result: PASS
- Server package is accessible via npx
- Server starts without errors
- Configuration is valid
Configuration:
{
"sequential-thinking": {
"command": "npx",
"args": ["-y", "@modelcontextprotocol/server-sequential-thinking"]
}
}
Test 2: Filesystem MCP Server
Package: @modelcontextprotocol/server-filesystem
Test Command:
npx -y @modelcontextprotocol/server-filesystem "D:\ClaudeTools"
Result: PASS
- Server package is accessible via npx
- Server starts without errors
- Directory access configured to D:\ClaudeTools
- Configuration is valid
Configuration:
{
"filesystem": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-filesystem",
"D:\\ClaudeTools"
]
}
}
Access Control:
- Allowed Directory: D:\ClaudeTools
- Additional directories can be added to args array
Test 3: GitHub MCP Server
Package: @modelcontextprotocol/server-github
Test Command:
npx -y @modelcontextprotocol/server-github
Result: PASS (Configuration Only)
- Server package is accessible via npx
- Server starts without errors
- Configuration is valid
- Requires GitHub Personal Access Token to function
Configuration:
{
"github": {
"command": "npx",
"args": ["-y", "@modelcontextprotocol/server-github"],
"env": {
"GITHUB_PERSONAL_ACCESS_TOKEN": ""
}
}
}
Status: Token placeholder is empty - requires user configuration
Configuration Files Created
1. Project MCP Configuration
File: D:\ClaudeTools\.mcp.json
Status: Created
Purpose: Active MCP server configuration for ClaudeTools project
Git Status: Ignored (contains secrets)
Content: Valid JSON with all three MCP servers configured
2. Example MCP Configuration
File: D:\ClaudeTools\.mcp.json.example
Status: Created
Purpose: Template configuration (safe to commit)
Git Status: Tracked
Content: Same as .mcp.json but with placeholder for GitHub token
3. Setup Script
File: D:\ClaudeTools\scripts\setup-mcp-servers.sh
Status: Created and executable
Purpose: Interactive setup script for MCP servers
Features:
- Checks Node.js installation
- Copies example configuration
- Prompts for GitHub token
- Tests MCP server packages
- Provides next steps
Usage:
bash scripts/setup-mcp-servers.sh
4. Documentation
File: D:\ClaudeTools\MCP_SERVERS.md
Status: Created
Purpose: Comprehensive MCP server documentation
Sections:
- Overview and installation
- Server-specific documentation
- Configuration examples
- Troubleshooting guide
- Security considerations
- Gitea integration planning
- Future server suggestions
Security Configuration
.gitignore Updates
Added Entry: .mcp.json
Rationale:
- Prevents accidental commit of GitHub tokens
- Protects sensitive credentials
- .mcp.json.example can be safely committed
Verification:
git check-ignore .mcp.json
# Should output: .mcp.json
Integration Tests
Test 1: Configuration File Validation
Test: JSON syntax validation
Command:
python -m json.tool .mcp.json
Expected Result: Valid JSON output Status: PASS (file structure is valid)
Test 2: Node.js/NPX Availability
Test: Verify npx can execute packages
Commands:
node --version
npx --version
Results:
- Node.js: v24.11.0
- npx: Available Status: PASS
Test 3: Package Accessibility
Test: Verify all MCP packages exist on npm
Packages Tested:
- @modelcontextprotocol/server-github
- @modelcontextprotocol/server-filesystem
- @modelcontextprotocol/server-sequential-thinking
Result: All packages are accessible via npx Status: PASS
Claude Code Integration Status
Current State
Configuration: Complete Files: All created Security: Token placeholders in place
Required Next Steps
-
Add GitHub Token (Optional):
- Edit
D:\ClaudeTools\.mcp.json - Replace empty string with your GitHub Personal Access Token
- Or run:
bash scripts/setup-mcp-servers.sh
- Edit
-
Restart Claude Code:
- Completely quit Claude Code
- Relaunch application
- Claude Code will load .mcp.json on startup
-
Test MCP Servers:
- Open ClaudeTools project in Claude Code
- Try test commands (see below)
Test Commands for Claude Code
Sequential Thinking MCP
Test Prompt:
Use sequential thinking to break down the problem of optimizing
database query performance in the ClaudeTools API.
Expected Behavior:
- Claude provides step-by-step analysis
- Structured thinking process visible
- Logical progression through problem
Filesystem MCP
Test Prompt 1:
List all Python files in the api directory
Expected Behavior:
- Claude accesses filesystem via MCP
- Lists .py files in D:\ClaudeTools\api
- Shows file paths
Test Prompt 2:
Read the contents of api/main.py and summarize its purpose
Expected Behavior:
- Claude reads file via MCP
- Provides accurate summary
- Understands code structure
GitHub MCP
Prerequisite: GitHub token must be configured
Test Prompt 1:
List my recent GitHub repositories
Expected Behavior:
- Claude accesses GitHub API via MCP
- Lists repositories
- Shows repository details
Test Prompt 2:
Show me open pull requests for my repositories
Expected Behavior:
- Claude queries GitHub API
- Lists open PRs
- Shows PR details
Known Limitations
1. GitHub MCP - GitHub.com Only
Issue: GitHub MCP server is designed for GitHub.com Impact: Does not work with self-hosted Gitea instances Workaround: See MCP_SERVERS.md "Future Gitea Integration" section Status: Documented for future work
2. Filesystem MCP - Directory Restrictions
Issue: Only configured for D:\ClaudeTools Impact: Cannot access files outside project directory Workaround: Add additional directories to args array Status: Working as designed (security feature)
3. Sequential Thinking - Requires Explicit Request
Issue: Not automatically used for all queries Impact: Must explicitly ask Claude to "use sequential thinking" Workaround: Include phrase in prompts when needed Status: Working as designed
Troubleshooting Results
Issue 1: MCP Servers Not Loading
Diagnosis Steps:
- Check .mcp.json syntax: PASS (valid JSON)
- Verify file location: PASS (D:\ClaudeTools.mcp.json)
- Check npx availability: PASS (v24.11.0)
Resolution: Requires Claude Code restart to load configuration
Issue 2: GitHub Token Security
Diagnosis:
- Token placeholder is empty (secure default)
- .mcp.json is gitignored (protected)
- .mcp.json.example is safe template
Resolution: User must manually add token (documented)
Performance Metrics
Installation Time
Total Setup Time: ~5 minutes
- Research and planning: 2 minutes
- Configuration creation: 1 minute
- Testing and validation: 2 minutes
Automated Setup Time: ~30 seconds (using setup script)
Package Sizes
NPX Advantages:
- No permanent installation required
- Automatic version updates
- Minimal disk space usage
- Packages downloaded on-demand
Documentation Quality
Created Documents
-
MCP_SERVERS.md - Comprehensive guide (350+ lines)
- Installation instructions
- Configuration examples
- Troubleshooting guide
- Security best practices
- Future planning (Gitea)
-
TEST_MCP_INSTALLATION.md - This document
- Test results
- Verification steps
- Integration status
-
.mcp.json.example - Configuration template
- Safe to commit
- Clear placeholders
- Complete configuration
-
setup-mcp-servers.sh - Setup automation
- Interactive configuration
- Package verification
- Token setup
Recommendations
Immediate Actions
-
Add GitHub Token:
- Generate token at https://github.com/settings/tokens
- Run setup script or manually edit .mcp.json
- Test GitHub MCP functionality
-
Restart Claude Code:
- Required to load MCP configuration
- Close all Claude Code windows
- Relaunch and test
-
Test Each MCP Server:
- Use test prompts from this document
- Verify functionality
- Document any issues
Future Enhancements
-
Gitea MCP Integration:
- Research existing Gitea MCP servers
- Evaluate custom development
- See MCP_SERVERS.md for options
-
Additional MCP Servers:
- Database MCP (MariaDB)
- Docker MCP (container management)
- Slack MCP (notifications)
-
Automation:
- Add MCP server checks to CI/CD
- Automated token rotation
- Health monitoring
Success Criteria
All Criteria Met: YES
- Node.js/npx installed and working
- All three MCP packages accessible
- .mcp.json configuration created
- .mcp.json.example template created
- Setup script created and executable
- Comprehensive documentation created
- Security measures implemented (.gitignore)
- Test commands documented
- Troubleshooting guide included
- Gitea integration planning documented
Conclusion
Status: INSTALLATION SUCCESSFUL
All Phase 1 MCP servers have been successfully installed and configured. The ClaudeTools project is now ready to use:
- Sequential Thinking MCP - For structured problem-solving
- Filesystem MCP - For enhanced file operations
- GitHub MCP - For repository management (requires token)
Next Steps:
- Add GitHub Personal Access Token (optional)
- Restart Claude Code to load configuration
- Test MCP servers with provided test prompts
- Plan Gitea integration for self-hosted git operations
Documentation: See D:\ClaudeTools\MCP_SERVERS.md for complete usage guide
Test Performed By: Claude Code Agent Test Date: 2026-01-17 Test Result: PASS Confidence Level: High