feat: Complete sync of all Claude Code CLI upgrades

- Add all 21 commands (clawd, ralph, prometheus*, dexto*)
- Add all hooks (intelligent-router, clawd-*, prometheus-wrapper, unified-integration-v2)
- Add skills (ralph, prometheus master)
- Add MCP servers (registry.json, manager.sh)
- Add plugins directory with marketplaces
- Add health-check.sh and aliases.sh scripts
- Complete repository synchronization with local ~/.claude/

Total changes: 100+ new files added
All integrations now fully backed up in repository

🤖 Generated with Claude Code
Co-Authored-By: Claude <noreply@anthropic.com>

commands/prometheus.md

@@ -0,0 +1,105 @@
+---
+description: Delegate to Prometheus multi-agent code analysis system for issue resolution, feature implementation, and intelligent code context retrieval
+disable-model-invocation: true
+---
+
+# Prometheus Multi-Agent Code Analysis System
+
+Prometheus is a production-ready AI-powered platform that uses multi-agent systems and unified knowledge graphs to perform intelligent operations on codebases.
+
+## Capabilities
+
+- **Automated Issue Resolution**: End-to-end bug fixing with reproduction, patch generation, and validation
+- **Feature Implementation**: Context-aware feature analysis and implementation planning
+- **Intelligent Context Retrieval**: Graph-based semantic search over codebase structure
+- **Multi-Agent Orchestration**: Coordinated workflow between specialized agents
+- **Knowledge Graph Integration**: Neo4j-powered code representation
+- **Question Answering**: Natural language queries with tool-augmented agents
+
+## Agent Types
+
+1. **Issue Classifier**: Categorizes incoming issues (bug/feature/question/doc)
+2. **Bug Analyzer**: Analyzes and reproduces bugs
+3. **Feature Analyzer**: Plans feature implementations
+4. **Context Provider**: Retrieves relevant code context
+5. **Edit Generator**: Creates code patches
+6. **Test Runner**: Validates changes in containerized environment
+
+## Usage
+
+### Basic Issue Analysis
+
+```bash
+/prometheus "Analyze this issue: Login fails after password reset"
+```
+
+### Bug Fix Mode
+
+```bash
+/prometheus --bug "Fix the authentication bug in src/auth/login.py"
+```
+
+### Feature Implementation
+
+```bash
+/prometheus --feature "Implement two-factor authentication"
+```
+
+### Code Context Query
+
+```bash
+/prometheus --query "How does the payment processing work?"
+```
+
+### With Repository
+
+```bash
+/prometheus --repo /path/to/repo "Analyze the codebase structure"
+```
+
+## Integration Points
+
+- **Knowledge Graph**: Neo4j for code structure and semantic analysis
+- **Docker**: Containerized testing environment
+- **Git**: Version control operations
+- **AST Parsing**: Multi-language code analysis
+- **LangGraph**: State machine orchestration
+
+## Output
+
+Prometheus provides:
+- Issue classification and analysis
+- Bug reproduction steps
+- Generated patches with validation
+- Context-aware recommendations
+- Test results and coverage
+
+## Examples
+
+```bash
+# Analyze a GitHub issue
+/prometheus "Issue #123: Memory leak in data processing pipeline"
+
+# Implement a feature
+/prometheus --feature "Add rate limiting to API endpoints"
+
+# Code understanding
+/prometheus --query "Explain the authentication flow"
+
+# Bug fix with context
+/prometheus --bug --repo ./myapp "Fix null pointer in user service"
+```
+
+## Configuration
+
+Prometheus uses:
+- `~/.claude/prometheus/` - Installation directory
+- `~/.claude/prometheus/venv/` - Python virtual environment
+- `~/.claude/prometheus/logs/` - Execution logs
+- Environment variables for API keys and Neo4j connection
+
+## User's Task
+
+Execute the following using Prometheus:
+
+{{USER_MESSAGE}}