refactor: consolidate documentation directories

Merged claudedocs/ into docs/research/ for consistent documentation structure.

Changes:
- Moved all claudedocs/*.md files to docs/research/
- Updated all path references in documentation (EN/KR)
- Updated RULES.md and research.md command templates
- Removed claudedocs/ directory
- Removed ClaudeDocs/ from .gitignore

Benefits:
- Single source of truth for all research reports
- PEP8-compliant lowercase directory naming
- Clearer documentation organization
- Prevents future claudedocs/ directory creation

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

docs/research/mcp-installer-fix-summary.md

@@ -0,0 +1,117 @@
+# MCP Installer Fix Summary
+
+## Problem Identified
+The SuperClaude Framework installer was using `claude mcp add` CLI commands which are designed for Claude Desktop, not Claude Code. This caused installation failures.
+
+## Root Cause
+- Original implementation: Used `claude mcp add` CLI commands
+- Issue: CLI commands are unreliable with Claude Code
+- Best Practice: Claude Code prefers direct JSON file manipulation at `~/.claude/mcp.json`
+
+## Solution Implemented
+
+### 1. JSON-Based Helper Methods (Lines 213-302)
+Created new helper methods for JSON-based configuration:
+- `_get_claude_code_config_file()`: Get config file path
+- `_load_claude_code_config()`: Load JSON configuration
+- `_save_claude_code_config()`: Save JSON configuration
+- `_register_mcp_server_in_config()`: Register server in config
+- `_unregister_mcp_server_from_config()`: Unregister server from config
+
+### 2. Updated Installation Methods
+
+#### `_install_mcp_server()` (npm-based servers)
+- **Before**: Used `claude mcp add -s user {server_name} {command} {args}`
+- **After**: Direct JSON configuration with `command` and `args` fields
+- **Config Format**:
+```json
+{
+  "command": "npx",
+  "args": ["-y", "@package/name"],
+  "env": {
+    "API_KEY": "value"
+  }
+}
+```
+
+#### `_install_docker_mcp_gateway()` (Docker Gateway)
+- **Before**: Used `claude mcp add -s user -t sse {server_name} {url}`
+- **After**: Direct JSON configuration with `url` field for SSE transport
+- **Config Format**:
+```json
+{
+  "url": "http://localhost:9090/sse",
+  "description": "Dynamic MCP Gateway for zero-token baseline"
+}
+```
+
+#### `_install_github_mcp_server()` (GitHub/uvx servers)
+- **Before**: Used `claude mcp add -s user {server_name} {run_command}`
+- **After**: Parse run command and create JSON config with `command` and `args`
+- **Config Format**:
+```json
+{
+  "command": "uvx",
+  "args": ["--from", "git+https://github.com/..."]
+}
+```
+
+#### `_install_uv_mcp_server()` (uv-based servers)
+- **Before**: Used `claude mcp add -s user {server_name} {run_command}`
+- **After**: Parse run command and create JSON config
+- **Special Case**: Serena server includes project-specific `--project` argument
+- **Config Format**:
+```json
+{
+  "command": "uvx",
+  "args": ["--from", "git+...", "serena", "start-mcp-server", "--project", "/path/to/project"]
+}
+```
+
+#### `_uninstall_mcp_server()` (Uninstallation)
+- **Before**: Used `claude mcp remove {server_name}`
+- **After**: Direct JSON configuration removal via `_unregister_mcp_server_from_config()`
+
+### 3. Updated Check Method
+#### `_check_mcp_server_installed()`
+- **Before**: Used `claude mcp list` CLI command
+- **After**: Reads `~/.claude/mcp.json` directly and checks `mcpServers` section
+- **Special Case**: For AIRIS Gateway, also verifies SSE endpoint is responding
+
+## Benefits
+1. **Reliability**: Direct JSON manipulation is more reliable than CLI commands
+2. **Compatibility**: Works correctly with Claude Code
+3. **Performance**: No subprocess calls for registration
+4. **Consistency**: Follows AIRIS MCP Gateway working pattern
+
+## Testing Required
+- Test npm-based server installation (sequential-thinking, context7, magic)
+- Test Docker Gateway installation (airis-mcp-gateway)
+- Test GitHub/uvx server installation (serena)
+- Test server uninstallation
+- Verify config file format at `~/.claude/mcp.json`
+
+## Files Modified
+- `/Users/kazuki/github/SuperClaude_Framework/setup/components/mcp.py`
+  - Added JSON helper methods (lines 213-302)
+  - Updated `_check_mcp_server_installed()` (lines 357-381)
+  - Updated `_install_mcp_server()` (lines 509-611)
+  - Updated `_install_docker_mcp_gateway()` (lines 571-747)
+  - Updated `_install_github_mcp_server()` (lines 454-569)
+  - Updated `_install_uv_mcp_server()` (lines 325-452)
+  - Updated `_uninstall_mcp_server()` (lines 972-987)
+
+## Reference Implementation
+AIRIS MCP Gateway Makefile pattern:
+```makefile
+install-claude: ## Install and register with Claude Code
+    @mkdir -p $(HOME)/.claude
+    @rm -f $(HOME)/.claude/mcp.json
+    @ln -s $(PWD)/mcp.json $(HOME)/.claude/mcp.json
+```
+
+## Next Steps
+1. Test the modified installer with a clean Claude Code environment
+2. Verify all server types install correctly
+3. Check that uninstallation works properly
+4. Update documentation if needed