feat: Major directory reorganization and cleanup

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>
2026-01-18 20:42:28 -07:00
parent 89e5118306
commit 06f7617718
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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:
+
+1. **GitHub MCP Server** - Configured (requires token)
+2. **Filesystem MCP Server** - Configured and ready
+3. **Sequential Thinking MCP Server** - Configured and ready
+
+---
+
+## Package Verification Tests
+
+### Test 1: Sequential Thinking MCP Server
+
+**Package:** `@modelcontextprotocol/server-sequential-thinking`
+
+**Test Command:**
+```bash
+npx -y @modelcontextprotocol/server-sequential-thinking
+```
+
+**Result:** PASS
+- Server package is accessible via npx
+- Server starts without errors
+- Configuration is valid
+
+**Configuration:**
+```json
+{
+  "sequential-thinking": {
+    "command": "npx",
+    "args": ["-y", "@modelcontextprotocol/server-sequential-thinking"]
+  }
+}
+```
+
+---
+
+### Test 2: Filesystem MCP Server
+
+**Package:** `@modelcontextprotocol/server-filesystem`
+
+**Test Command:**
+```bash
+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:**
+```json
+{
+  "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:**
+```bash
+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:**
+```json
+{
+  "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
+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:**
+```bash
+git check-ignore .mcp.json
+# Should output: .mcp.json
+```
+
+---
+
+## Integration Tests
+
+### Test 1: Configuration File Validation
+
+**Test:** JSON syntax validation
+
+**Command:**
+```bash
+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:**
+```bash
+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
+
+1. **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`
+
+2. **Restart Claude Code:**
+   - Completely quit Claude Code
+   - Relaunch application
+   - Claude Code will load .mcp.json on startup
+
+3. **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:**
+1. Check .mcp.json syntax: PASS (valid JSON)
+2. Verify file location: PASS (D:\ClaudeTools\.mcp.json)
+3. 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
+
+1. **MCP_SERVERS.md** - Comprehensive guide (350+ lines)
+   - Installation instructions
+   - Configuration examples
+   - Troubleshooting guide
+   - Security best practices
+   - Future planning (Gitea)
+
+2. **TEST_MCP_INSTALLATION.md** - This document
+   - Test results
+   - Verification steps
+   - Integration status
+
+3. **.mcp.json.example** - Configuration template
+   - Safe to commit
+   - Clear placeholders
+   - Complete configuration
+
+4. **setup-mcp-servers.sh** - Setup automation
+   - Interactive configuration
+   - Package verification
+   - Token setup
+
+---
+
+## Recommendations
+
+### Immediate Actions
+
+1. **Add GitHub Token:**
+   - Generate token at https://github.com/settings/tokens
+   - Run setup script or manually edit .mcp.json
+   - Test GitHub MCP functionality
+
+2. **Restart Claude Code:**
+   - Required to load MCP configuration
+   - Close all Claude Code windows
+   - Relaunch and test
+
+3. **Test Each MCP Server:**
+   - Use test prompts from this document
+   - Verify functionality
+   - Document any issues
+
+---
+
+### Future Enhancements
+
+1. **Gitea MCP Integration:**
+   - Research existing Gitea MCP servers
+   - Evaluate custom development
+   - See MCP_SERVERS.md for options
+
+2. **Additional MCP Servers:**
+   - Database MCP (MariaDB)
+   - Docker MCP (container management)
+   - Slack MCP (notifications)
+
+3. **Automation:**
+   - Add MCP server checks to CI/CD
+   - Automated token rotation
+   - Health monitoring
+
+---
+
+## Success Criteria
+
+### All Criteria Met: YES
+
+- [X] Node.js/npx installed and working
+- [X] All three MCP packages accessible
+- [X] .mcp.json configuration created
+- [X] .mcp.json.example template created
+- [X] Setup script created and executable
+- [X] Comprehensive documentation created
+- [X] Security measures implemented (.gitignore)
+- [X] Test commands documented
+- [X] Troubleshooting guide included
+- [X] 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:
+
+1. **Sequential Thinking MCP** - For structured problem-solving
+2. **Filesystem MCP** - For enhanced file operations
+3. **GitHub MCP** - For repository management (requires token)
+
+**Next Steps:**
+1. Add GitHub Personal Access Token (optional)
+2. Restart Claude Code to load configuration
+3. Test MCP servers with provided test prompts
+4. 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