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>

mcp-servers/manager.sh

@@ -0,0 +1,164 @@
+#!/bin/bash
+# MCP Server Manager - Start, stop, and manage MCP servers
+
+set -euo pipefail
+
+MCP_DIR="${HOME}/.claude/mcp-servers"
+REGISTRY="${MCP_DIR}/registry.json"
+PID_DIR="${MCP_DIR}/pids"
+LOG_DIR="${MCP_DIR}/logs"
+
+mkdir -p "$PID_DIR" "$LOG_DIR"
+
+log() {
+    echo "[$(date -u +"%Y-%m-%d %H:%M:%S UTC")] [mcp-manager] $*" | tee -a "${LOG_DIR}/manager.log"
+}
+
+start_server() {
+    local server_name="$1"
+    local server_config
+    
+    # Get server config from registry
+    server_config=$(jq -r ".servers.${server_name}" "$REGISTRY" 2>/dev/null)
+    
+    if [[ "$server_config" == "null" ]]; then
+        log "ERROR: Server '${server_name}' not found in registry"
+        return 1
+    fi
+    
+    local enabled=$(echo "$server_config" | jq -r '.enabled // false')
+    if [[ "$enabled" != "true" ]]; then
+        log "Server '${server_name}' is disabled"
+        return 0
+    fi
+    
+    local pid_file="${PID_DIR}/${server_name}.pid"
+    
+    if [[ -f "$pid_file" ]]; then
+        local pid=$(cat "$pid_file")
+        if kill -0 "$pid" 2>/dev/null; then
+            log "Server '${server_name}' already running (PID: ${pid})"
+            return 0
+        fi
+    fi
+    
+    local command=$(echo "$server_config" | jq -r '.command')
+    local args=$(echo "$server_config" | jq -r '.args[]' | sed 's/^/"/;s/$/" ' | tr '\n' ' ')
+    
+    log "Starting server '${server_name}': ${command} ${args}"
+    
+    eval "nohup ${command} ${args} > ${LOG_DIR}/${server_name}.log 2>&1 &"
+    local pid=$!
+    echo "$pid" > "$pid_file"
+    sleep 1
+    
+    if kill -0 "$pid" 2>/dev/null; then
+        log "Server '${server_name}' started (PID: ${pid})"
+        return 0
+    else
+        log "ERROR: Failed to start server '${server_name}'"
+        return 1
+    fi
+}
+
+stop_server() {
+    local server_name="$1"
+    local pid_file="${PID_DIR}/${server_name}.pid"
+    
+    if [[ ! -f "$pid_file" ]]; then
+        log "Server '${server_name}' not running"
+        return 0
+    fi
+    
+    local pid=$(cat "$pid_file")
+    log "Stopping server '${server_name}' (PID: ${pid})..."
+    kill "$pid" 2>/dev/null || true
+    rm -f "$pid_file"
+    log "Server '${server_name}' stopped"
+}
+
+start_all() {
+    local servers=$(jq -r '.servers | keys[]' "$REGISTRY")
+    for server in $servers; do
+        start_server "$server" || true
+    done
+}
+
+stop_all() {
+    local pid_files
+    pid_files=$(ls "$PID_DIR"/*.pid 2>/dev/null || true)
+    
+    for pid_file in $pid_files; do
+        local server_name=$(basename "$pid_file" .pid)
+        stop_server "$server_name"
+    done
+}
+
+status() {
+    echo "=== MCP Server Status ==="
+    echo ""
+    
+    local servers=$(jq -r '.servers | keys[]' "$REGISTRY")
+    for server in $servers; do
+        local enabled=$(jq -r ".servers.${server}.enabled // false" "$REGISTRY")
+        local pid_file="${PID_DIR}/${server}.pid"
+        local status="stopped"
+        
+        if [[ -f "$pid_file" ]]; then
+            local pid=$(cat "$pid_file")
+            if kill -0 "$pid" 2>/dev/null; then
+                status="running (PID: ${pid})"
+            fi
+        fi
+        
+        local icon="🔴"
+        if [[ "$status" == "stopped" ]]; then
+            [[ "$enabled" == "true" ]] && icon="⚪" || icon="⏸️"
+        else
+            icon="🟢"
+        fi
+        
+        local name=$(jq -r ".servers.${server}.name" "$REGISTRY")
+        local category=$(jq -r ".servers.${server}.category // \"other\"" "$REGISTRY")
+        
+        printf "%s %-20s [%-10s] %s\n" "$icon" "$server" "$category" "$status"
+    done
+}
+
+main() {
+    local command="${1:-status}"
+    
+    case "$command" in
+        start)
+            if [[ -n "${2:-}" ]]; then
+                start_server "$2"
+            else
+                start_all
+            fi
+            ;;
+        stop)
+            if [[ -n "${2:-}" ]]; then
+                stop_server "$2"
+            else
+                stop_all
+            fi
+            ;;
+        restart)
+            stop_all
+            sleep 2
+            start_all
+            ;;
+        status)
+            status
+            ;;
+        list)
+            jq -r '.servers | keys[]' "$REGISTRY"
+            ;;
+        *)
+            echo "Usage: $0 {start|stop|restart|status|list} [server_name]"
+            exit 1
+            ;;
+    esac
+}
+
+main "$@"