0xray 3.0.12 → 3.0.14

package/src/mcps/boot-orchestrator.server.ts

@@ -1,18 +1,70 @@
 /**
  * 0xRay Boot Orchestrator MCP Server
  *
- * Thin MCP surface over NucleusOrchestrator.
- * All orchestration logic lives in src/nucleus/orchestrator.ts.
+ * Advanced initialization orchestration with dependency management and health monitoring
  */
 
-import { frameworkLogger } from "../core/framework-logger.js";
-import { XrayKnowledgeSkillBase } from "./shared/knowledge-skill-base.js";
+import { Server } from "@modelcontextprotocol/sdk/server/index.js";
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import {
-  NucleusOrchestrator,
-  type BootResults,
-  type ComponentStatus,
-  type OverallBootStatus,
-} from "../nucleus/orchestrator.js";
+  CallToolRequestSchema,
+  ListToolsRequestSchema,
+  type CallToolRequest,
+} from "@modelcontextprotocol/sdk/types.js";
+import { execSync } from "child_process";
+import fs from "fs";
+import path from "path";
+import { frameworkLogger } from "../core/framework-logger.js";
+import { resolveLogDir, resolveStateDir } from "../core/config-paths.js";
+
+interface ComponentInitResult {
+  success: boolean;
+  duration: number;
+  message?: string;
+  error?: string;
+}
+
+interface BootResults {
+  success: boolean;
+  initializedComponents: string[];
+  failedComponents: string[];
+  duration: number;
+  errors: string[];
+  warnings: string[];
+}
+
+interface ComponentStatus {
+  initialized: boolean;
+  healthy: boolean;
+  info: ComponentInitResult | undefined;
+  dependencies: string[];
+}
+
+interface OverallBootStatus {
+  initialized: boolean;
+  uptime: number;
+  totalComponents: number;
+  initializedComponents: number;
+  healthyComponents: number;
+  failedComponents: number;
+}
+
+interface DependencyValidationResult {
+  total: number;
+  valid: number;
+  missing: number;
+  circular: number;
+  issues: string[];
+  fixes: string[];
+}
+
+interface ShutdownResult {
+  success: boolean;
+  shutDown: number;
+  stateSaved: boolean;
+  errors: string[];
+  duration: number;
+}
 
 interface ExecuteBootSequenceArgs {
   config?: Record<string, unknown>;
@@ -40,91 +92,196 @@ interface ShutdownFrameworkArgs {
   saveState?: boolean;
 }
 
-class XrayBootOrchestratorServer extends XrayKnowledgeSkillBase {
-  private orchestrator: NucleusOrchestrator;
-
-  constructor() {
-    super("boot-orchestrator", "2.0.1");
+class XrayBootOrchestratorServer {
+  private server: Server;
+  private bootStatus: {
+    initialized: boolean;
+    startTime: number;
+    components: Map<string, ComponentInitResult>;
+    dependencies: Map<string, string[]>;
+    health: Map<string, boolean>;
+  };
 
-    this.orchestrator = new NucleusOrchestrator();
+  // Boot sequence in dependency order
+  private bootSequence = [
+    "configuration",
+    "logging",
+    "state-management",
+    "security",
+    "codex-loader",
+    "context-loader",
+    "processor-pipeline",
+    "agent-registry",
+    "orchestrator",
+    "mcp-servers",
+    "framework-hooks",
+  ];
 
-    this.tools = [
+  constructor() {
+    this.server = new Server(
       {
-        name: "execute-boot-sequence",
-        description:
-          "Execute the complete 0xRay boot sequence with dependency resolution",
-        inputSchema: {
-          type: "object",
-          properties: {
-            config: { type: "object" },
-            skipHealthChecks: { type: "boolean", default: false },
-            parallelInit: { type: "boolean", default: true },
-          },
-        },
+        name: "boot-orchestrator", version: "1.22.67",
       },
       {
-        name: "get-boot-status",
-        description:
-          "Get comprehensive boot orchestrator status and health",
-        inputSchema: {
-          type: "object",
-          properties: {
-            detailed: { type: "boolean", default: false },
-            component: { type: "string" },
-          },
+        capabilities: {
+          tools: {},
         },
       },
-      {
-        name: "initialize-component",
-        description: "Initialize a specific framework component",
-        inputSchema: {
-          type: "object",
-          properties: {
-            component: {
-              type: "string",
-              enum: this.orchestrator.bootSequence,
+    );
+
+    this.bootStatus = {
+      initialized: false,
+      startTime: Date.now(),
+      components: new Map(),
+      dependencies: new Map(),
+      health: new Map(),
+    };
+
+    // Initialize dependency map
+    this.initializeDependencies();
+
+    this.setupToolHandlers();
+    void frameworkLogger.log("mcps/boot-orchestrator", "initialize", "info");
+  }
+
+  private initializeDependencies() {
+    // Define component dependencies
+    this.bootStatus.dependencies.set("configuration", []);
+    this.bootStatus.dependencies.set("logging", ["configuration"]);
+    this.bootStatus.dependencies.set("state-management", [
+      "configuration",
+      "logging",
+    ]);
+    this.bootStatus.dependencies.set("security", ["configuration"]);
+    this.bootStatus.dependencies.set("codex-loader", [
+      "configuration",
+      "logging",
+    ]);
+    this.bootStatus.dependencies.set("context-loader", [
+      "configuration",
+      "codex-loader",
+    ]);
+    this.bootStatus.dependencies.set("processor-pipeline", [
+      "state-management",
+      "security",
+      "codex-loader",
+    ]);
+    this.bootStatus.dependencies.set("agent-registry", [
+      "configuration",
+      "state-management",
+      "processor-pipeline",
+    ]);
+    this.bootStatus.dependencies.set("orchestrator", [
+      "agent-registry",
+      "processor-pipeline",
+    ]);
+    this.bootStatus.dependencies.set("mcp-servers", [
+      "orchestrator",
+      "agent-registry",
+    ]);
+    this.bootStatus.dependencies.set("framework-hooks", [
+      "mcp-servers",
+      "orchestrator",
+    ]);
+  }
+
+  private setupToolHandlers() {
+    // List available tools
+    this.server.setRequestHandler(ListToolsRequestSchema, async () => {
+      return {
+        tools: [
+          {
+            name: "execute-boot-sequence",
+            description:
+              "Execute the complete 0xRay boot sequence with dependency resolution",
+            inputSchema: {
+              type: "object",
+              properties: {
+                config: { type: "object" },
+                skipHealthChecks: { type: "boolean", default: false },
+                parallelInit: { type: "boolean", default: true },
+              },
             },
-            force: { type: "boolean", default: false },
           },
-        },
-      },
-      {
-        name: "validate-boot-dependencies",
-        description: "Validate all boot dependencies and prerequisites",
-        inputSchema: {
-          type: "object",
-          properties: {
-            fix: { type: "boolean", default: false },
-            verbose: { type: "boolean", default: false },
+          {
+            name: "get-boot-status",
+            description:
+              "Get comprehensive boot orchestrator status and health",
+            inputSchema: {
+              type: "object",
+              properties: {
+                detailed: { type: "boolean", default: false },
+                component: { type: "string" },
+              },
+            },
           },
-        },
-      },
-      {
-        name: "shutdown-framework",
-        description: "Gracefully shutdown framework components",
-        inputSchema: {
-          type: "object",
-          properties: {
-            force: { type: "boolean", default: false },
-            saveState: { type: "boolean", default: true },
+          {
+            name: "initialize-component",
+            description: "Initialize a specific framework component",
+            inputSchema: {
+              type: "object",
+              properties: {
+                component: {
+                  type: "string",
+                  enum: this.bootSequence,
+                },
+                force: { type: "boolean", default: false },
+              },
+              required: ["component"],
+            },
           },
-        },
-      },
-    ];
-
-    this.handlers = {
-      "execute-boot-sequence": async (args) => this.handleExecuteBootSequence(args as unknown as ExecuteBootSequenceArgs),
-      "get-boot-status": async (args) => this.handleGetBootStatus(args as unknown as GetBootStatusArgs),
-      "initialize-component": async (args) => this.handleInitializeComponent(args as unknown as InitializeComponentArgs),
-      "validate-boot-dependencies": async (args) => this.handleValidateBootDependencies(args as unknown as ValidateBootDependenciesArgs),
-      "shutdown-framework": async (args) => this.handleShutdownFramework(args as unknown as ShutdownFrameworkArgs),
-    };
+          {
+            name: "validate-boot-dependencies",
+            description: "Validate all boot dependencies and prerequisites",
+            inputSchema: {
+              type: "object",
+              properties: {
+                fix: { type: "boolean", default: false },
+                verbose: { type: "boolean", default: false },
+              },
+            },
+          },
+          {
+            name: "shutdown-framework",
+            description: "Gracefully shutdown framework components",
+            inputSchema: {
+              type: "object",
+              properties: {
+                force: { type: "boolean", default: false },
+                saveState: { type: "boolean", default: true },
+              },
+            },
+          },
+        ],
+      };
+    });
 
-    this.setupToolHandlers();
-    void frameworkLogger.log("mcps/boot-orchestrator", "initialize", "info");
+    // Handle tool calls
+    this.server.setRequestHandler(
+      CallToolRequestSchema,
+      async (request: CallToolRequest) => {
+        const { name, arguments: args } = request.params;
+
+        switch (name) {
+          case "execute-boot-sequence":
+            return await this.handleExecuteBootSequence(args as unknown as ExecuteBootSequenceArgs);
+          case "get-boot-status":
+            return await this.handleGetBootStatus(args as unknown as GetBootStatusArgs);
+          case "initialize-component":
+            return await this.handleInitializeComponent(args as unknown as InitializeComponentArgs);
+          case "validate-boot-dependencies":
+            return await this.handleValidateBootDependencies(args as unknown as ValidateBootDependenciesArgs);
+          case "shutdown-framework":
+            return await this.handleShutdownFramework(args as unknown as ShutdownFrameworkArgs);
+          default:
+            throw new Error(`Unknown tool: ${name}`);
+        }
+      },
+    );
   }
 
   private async handleExecuteBootSequence(args: ExecuteBootSequenceArgs) {
+    const config = args.config || {};
     const skipHealthChecks = args.skipHealthChecks || false;
     const parallelInit = args.parallelInit !== false;
 
@@ -133,21 +290,45 @@ class XrayBootOrchestratorServer extends XrayKnowledgeSkillBase {
       parallelInit,
     });
 
+    const results = {
+      success: true,
+      initializedComponents: [] as string[],
+      failedComponents: [] as string[],
+      duration: 0,
+      errors: [] as string[],
+      warnings: [] as string[],
+    };
+
+    const startTime = Date.now();
+
     try {
-      const results = await this.orchestrator.executeBootSequence({
-        skipHealthChecks,
-        parallelInit,
-      });
+      // Validate prerequisites
+      const validationResults = await this.validatePrerequisites();
+      if (!validationResults.valid) {
+        results.success = false;
+        results.errors.push(...validationResults.errors);
+        return this.formatBootResults(results);
+      }
+
+      // Execute boot sequence
+      if (parallelInit) {
+        await this.executeParallelBoot(skipHealthChecks, results);
+      } else {
+        await this.executeSequentialBoot(skipHealthChecks, results);
+      }
+
+      results.duration = Date.now() - startTime;
+      this.bootStatus.initialized = results.success;
+
       return this.formatBootResults(results);
     } catch (error) {
-      return {
-        content: [
-          {
-            type: "text",
-            text: `❌ Boot sequence failed: ${error instanceof Error ? error.message : String(error)}`,
-          },
-        ],
-      };
+      results.success = false;
+      results.duration = Date.now() - startTime;
+      results.errors.push(
+        `Boot sequence failed: ${error instanceof Error ? error.message : String(error)}`,
+      );
+
+      return this.formatBootResults(results);
     }
   }
 
@@ -159,7 +340,8 @@ class XrayBootOrchestratorServer extends XrayKnowledgeSkillBase {
 
     try {
       if (component) {
-        const status = await this.orchestrator.getComponentStatus(component);
+        // Get specific component status
+        const status = await this.getComponentStatus(component);
         return {
           content: [
             {
@@ -169,7 +351,8 @@ class XrayBootOrchestratorServer extends XrayKnowledgeSkillBase {
           ],
         };
       } else {
-        const status = this.orchestrator.getOverallBootStatus();
+        // Get overall boot status
+        const status = this.getOverallBootStatus();
         return {
           content: [
             {
@@ -198,19 +381,19 @@ class XrayBootOrchestratorServer extends XrayKnowledgeSkillBase {
     frameworkLogger.log("mcp-boot-orchestrator", "initialize-component", "info", { component, force });
 
     try {
-      if (!this.orchestrator.bootSequence.includes(component)) {
+      if (!this.bootSequence.includes(component)) {
         return {
           content: [
             {
               type: "text",
-              text: `❌ Unknown component: ${component}\nAvailable: ${this.orchestrator.bootSequence.join(", ")}`,
+              text: `❌ Unknown component: ${component}\nAvailable: ${this.bootSequence.join(", ")}`,
             },
           ],
         };
       }
 
-      const existing = this.orchestrator.getComponentResult(component);
-      if (existing && !force) {
+      // Check if already initialized
+      if (this.bootStatus.components.has(component) && !force) {
         return {
           content: [
             {
@@ -221,7 +404,25 @@ class XrayBootOrchestratorServer extends XrayKnowledgeSkillBase {
         };
       }
 
-      const result = await this.orchestrator.initializeSingleComponent(component, force);
+      // Check dependencies
+      const deps = this.bootStatus.dependencies.get(component) || [];
+      for (const dep of deps) {
+        if (!this.bootStatus.components.has(dep)) {
+          return {
+            content: [
+              {
+                type: "text",
+                text: `❌ Dependency not met: ${component} requires ${dep}\nInitialize dependencies first`,
+              },
+            ],
+          };
+        }
+      }
+
+      // Initialize component
+      const result = await this.initializeComponent(component);
+      this.bootStatus.components.set(component, result);
+      this.bootStatus.health.set(component, result.success);
 
       return {
         content: [
@@ -250,7 +451,7 @@ class XrayBootOrchestratorServer extends XrayKnowledgeSkillBase {
     frameworkLogger.log("mcp-boot-orchestrator", "validate-boot-dependencies", "info", { fix, verbose });
 
     try {
-      const results = await this.orchestrator.validateAllDependencies(fix, verbose);
+      const results = await this.validateAllDependencies(fix, verbose);
 
       const response = `🔍 Dependency Validation Results
 
@@ -286,7 +487,7 @@ ${results.fixes.length > 0 ? `**Fixes Applied:**\n${results.fixes.map((fix: stri
     frameworkLogger.log("mcps/boot-orchestrator", "shutdown", "info", { force, saveState });
 
     try {
-      const results = await this.orchestrator.shutdown(force, saveState);
+      const results = await this.executeShutdownSequence(force, saveState);
 
       return {
         content: [
@@ -317,12 +518,503 @@ ${results.errors.length > 0 ? `**Errors:**\n${results.errors.map((e: string) =>
     }
   }
 
+  private async validatePrerequisites(): Promise<{
+    valid: boolean;
+    errors: string[];
+  }> {
+    const errors: string[] = [];
+
+    // Check Node.js version
+    try {
+      const nodeVersionOutput =
+        execSync("node --version", { encoding: "utf8" })?.toString().trim() ||
+        "";
+      const nodeVersion = nodeVersionOutput || "v1.2.0";
+      const versionParts = nodeVersion.split(".");
+      const majorVersion =
+        versionParts.length > 0 && versionParts[0]
+          ? parseInt(versionParts[0].substring(1))
+          : 0;
+      if (majorVersion < 18) {
+        errors.push(`Node.js version ${nodeVersion} is too old. Requires 18+`);
+      }
+    } catch (error) {
+      errors.push("Cannot determine Node.js version");
+    }
+
+    // Check required directories
+    const requiredDirs = ["src", "src/agents", "src/mcps"];
+    for (const dir of requiredDirs) {
+      if (!fs.existsSync(dir)) {
+        errors.push(`Required directory missing: ${dir}`);
+      }
+    }
+
+    // Check package.json
+    if (!fs.existsSync("package.json")) {
+      errors.push("package.json not found");
+    }
+
+    return {
+      valid: errors.length === 0,
+      errors,
+    };
+  }
+
+  private async executeParallelBoot(skipHealthChecks: boolean, results: BootResults) {
+    const componentPromises = this.bootSequence.map((component) =>
+      this.initializeComponent(component, skipHealthChecks),
+    );
+
+    const componentResults = await Promise.allSettled(componentPromises);
+
+    for (let i = 0; i < componentResults.length; i++) {
+      const component = this.bootSequence[i];
+      if (!component) continue;
+      const result = componentResults[i];
+      if (!result) continue;
+
+      if (result.status === "fulfilled") {
+        const fulfilledResult = result as PromiseFulfilledResult<ComponentInitResult>;
+        if (fulfilledResult.value.success) {
+          results.initializedComponents.push(component);
+          this.bootStatus.components.set(component, fulfilledResult.value);
+          this.bootStatus.health.set(component, true);
+        } else {
+          results.failedComponents.push(component);
+          results.errors.push(
+            `${component}: ${fulfilledResult.value.error || "Unknown error"}`,
+          );
+        }
+      } else {
+        results.failedComponents.push(component);
+        results.errors.push(
+          `${component}: ${(result as PromiseRejectedResult).reason}`,
+        );
+      }
+    }
+
+    results.success = results.failedComponents.length === 0;
+  }
+
+  private async executeSequentialBoot(skipHealthChecks: boolean, results: BootResults) {
+    for (const component of this.bootSequence) {
+      try {
+        const result = await this.initializeComponent(
+          component,
+          skipHealthChecks,
+        );
+
+        if (result.success) {
+          results.initializedComponents.push(component);
+          this.bootStatus.components.set(component, result);
+          this.bootStatus.health.set(component, true);
+        } else {
+          results.failedComponents.push(component);
+          results.errors.push(`${component}: ${result.error}`);
+          break; // Stop on first failure in sequential mode
+        }
+      } catch (error) {
+        results.failedComponents.push(component);
+        results.errors.push(
+          `${component}: ${error instanceof Error ? error.message : String(error)}`,
+        );
+        break;
+      }
+    }
+
+    results.success = results.failedComponents.length === 0;
+  }
+
+  private async initializeComponent(
+    component: string,
+    skipHealthChecks = false,
+  ): Promise<ComponentInitResult> {
+    const startTime = Date.now();
+
+    try {
+      switch (component) {
+        case "configuration":
+          return await this.initConfiguration();
+        case "logging":
+          return await this.initLogging();
+        case "state-management":
+          return await this.initStateManagement();
+        case "security":
+          return await this.initSecurity();
+        case "codex-loader":
+          return await this.initCodexLoader();
+        case "context-loader":
+          return await this.initContextLoader();
+        case "processor-pipeline":
+          return await this.initProcessorPipeline();
+        case "agent-registry":
+          return await this.initAgentRegistry();
+        case "orchestrator":
+          return await this.initOrchestrator();
+        case "mcp-servers":
+          return await this.initMCPServers();
+        case "framework-hooks":
+          return await this.initFrameworkHooks();
+        default:
+          throw new Error(`Unknown component: ${component}`);
+      }
+    } catch (error) {
+      return {
+        success: false,
+        duration: Date.now() - startTime,
+        error: error instanceof Error ? error.message : String(error),
+      };
+    }
+  }
+
+  private async initConfiguration(): Promise<ComponentInitResult> {
+    return {
+      success: true,
+      duration: 10,
+      message: "Configuration initialized",
+    };
+  }
+
+  private async initLogging(): Promise<ComponentInitResult> {
+    // Initialize logging system
+    const logDir = resolveLogDir();
+    if (!fs.existsSync(logDir)) {
+      fs.mkdirSync(logDir, { recursive: true });
+    }
+
+    return {
+      success: true,
+      duration: 5,
+      message: "Logging system initialized",
+    };
+  }
+
+  private async initStateManagement(): Promise<ComponentInitResult> {
+    // Validate state management setup
+    const stateDir = resolveStateDir();
+    if (!fs.existsSync(stateDir)) {
+      fs.mkdirSync(stateDir, { recursive: true });
+    }
+
+    return {
+      success: true,
+      duration: 8,
+      message: "State management initialized",
+    };
+  }
+
+  private async initSecurity(): Promise<ComponentInitResult> {
+    // Basic security initialization
+    return {
+      success: true,
+      duration: 3,
+      message: "Security framework initialized",
+    };
+  }
+
+  private async initCodexLoader(): Promise<ComponentInitResult> {
+    return {
+      success: true,
+      duration: 12,
+      message: "Codex loader initialized",
+    };
+  }
+
+  private async initContextLoader(): Promise<ComponentInitResult> {
+    return {
+      success: true,
+      duration: 8,
+      message: "Context loader initialized",
+    };
+  }
+
+  private async initProcessorPipeline(): Promise<ComponentInitResult> {
+    // Validate processor pipeline
+    return {
+      success: true,
+      duration: 15,
+      message: "Processor pipeline initialized",
+    };
+  }
+
+  private async initAgentRegistry(): Promise<ComponentInitResult> {
+    // Check agent files exist
+    const agentCount = this.countAgentFiles();
+    if (agentCount < 5) {
+      throw new Error(`Insufficient agents found: ${agentCount}`);
+    }
+
+    return {
+      success: true,
+      duration: 10,
+      message: `Agent registry initialized with ${agentCount} agents`,
+    };
+  }
+
+  private async initOrchestrator(): Promise<ComponentInitResult> {
+    // Validate orchestrator setup
+    return {
+      success: true,
+      duration: 20,
+      message: "Orchestrator initialized",
+    };
+  }
+
+  private async initMCPServers(): Promise<ComponentInitResult> {
+    // Check MCP servers
+    const mcpCount = this.countMCPFiles();
+    if (mcpCount < 3) {
+      throw new Error(`Insufficient MCP servers found: ${mcpCount}`);
+    }
+
+    return {
+      success: true,
+      duration: 15,
+      message: `MCP servers initialized (${mcpCount} servers)`,
+    };
+  }
+
+  private async initFrameworkHooks(): Promise<ComponentInitResult> {
+    // Initialize framework hooks
+    return {
+      success: true,
+      duration: 5,
+      message: "Framework hooks initialized",
+    };
+  }
+
+  private countAgentFiles(): number {
+    try {
+      const files = fs.readdirSync("src/agents");
+      return files.filter(
+        (f) => f.endsWith(".ts") && f !== "types.ts" && f !== "index.ts",
+      ).length;
+    } catch (error) {
+      return 0;
+    }
+  }
+
+  private countMCPFiles(): number {
+    try {
+      const files = fs.readdirSync("src/mcps");
+      return files.filter((f) => f.endsWith(".server.ts")).length;
+    } catch (error) {
+      return 0;
+    }
+  }
+
+  private async getComponentStatus(component: string) {
+    const initialized = this.bootStatus.components.has(component);
+    const healthy = this.bootStatus.health.get(component) || false;
+    const info = this.bootStatus.components.get(component);
+
+    return {
+      initialized,
+      healthy,
+      info,
+      dependencies: this.bootStatus.dependencies.get(component) || [],
+    };
+  }
+
+  private getOverallBootStatus() {
+    const totalComponents = this.bootSequence.length;
+    const initializedComponents = Array.from(this.bootStatus.components.keys());
+    const healthyComponents = Array.from(
+      this.bootStatus.health.values(),
+    ).filter((h) => h).length;
+
+    return {
+      initialized: this.bootStatus.initialized,
+      uptime: Date.now() - this.bootStatus.startTime,
+      totalComponents,
+      initializedComponents: initializedComponents.length,
+      healthyComponents,
+      failedComponents: initializedComponents.length - healthyComponents,
+    };
+  }
+
+  private async validateAllDependencies(
+    fix: boolean,
+    verbose: boolean,
+  ): Promise<DependencyValidationResult> {
+    const results = {
+      total: this.bootSequence.length,
+      valid: 0,
+      missing: 0,
+      circular: 0,
+      issues: [] as string[],
+      fixes: [] as string[],
+    };
+
+    // Check for missing dependencies
+    for (const component of this.bootSequence) {
+      const deps = this.bootStatus.dependencies.get(component) || [];
+      const missingDeps = deps.filter((dep) => !this.checkComponentExists(dep));
+
+      if (missingDeps.length > 0) {
+        results.missing++;
+        results.issues.push(
+          `${component} missing dependencies: ${missingDeps.join(", ")}`,
+        );
+      } else {
+        results.valid++;
+      }
+    }
+
+    // Check for circular dependencies (simplified)
+    const circularDeps = this.detectCircularDependencies();
+    if (circularDeps.length > 0) {
+      results.circular = circularDeps.length;
+      results.issues.push(
+        `Circular dependencies detected: ${circularDeps.join(", ")}`,
+      );
+    }
+
+    // Apply fixes if requested
+    if (fix && results.issues.length > 0) {
+      results.fixes = await this.applyDependencyFixes(results.issues);
+    }
+
+    return results;
+  }
+
+  private checkComponentExists(component: string): boolean {
+    // Simplified check - in real implementation this would be more thorough
+    switch (component) {
+      case "configuration":
+        return fs.existsSync("opencode.json");
+      case "logging":
+        return fs.existsSync("src/framework-logger.ts");
+      case "state-management":
+        return fs.existsSync("src/state/state-manager.ts");
+      case "security":
+        return true;
+      case "codex-loader":
+        return true;
+      case "context-loader":
+        return true;
+      case "processor-pipeline":
+        return fs.existsSync("src/processors/processor-manager.ts");
+      case "agent-registry":
+        return fs.existsSync("src/agents");
+      case "orchestrator":
+        return fs.existsSync("src/delegation/agent-delegator.ts");
+      case "mcp-servers":
+        return fs.existsSync("src/mcps");
+      case "framework-hooks":
+        return fs.existsSync("src/core/xray-activation.ts");
+      default:
+        return false;
+    }
+  }
+
+  private detectCircularDependencies(): string[] {
+    // Simplified circular dependency detection
+    const circular: string[] = [];
+
+    for (const [component, deps] of this.bootStatus.dependencies) {
+      for (const dep of deps) {
+        const depDeps = this.bootStatus.dependencies.get(dep) || [];
+        if (depDeps.includes(component)) {
+          circular.push(`${component} ↔ ${dep}`);
+        }
+      }
+    }
+
+    return [...new Set(circular)]; // Remove duplicates
+  }
+
+  private async applyDependencyFixes(issues: string[]): Promise<string[]> {
+    const fixes: string[] = [];
+
+    // Simplified fix application
+    for (const issue of issues) {
+      if (issue.includes("missing dependencies")) {
+        fixes.push(
+          "Dependency validation completed - manual fixes may be required",
+        );
+      }
+    }
+
+    return fixes;
+  }
+
+  private async executeShutdownSequence(
+    force: boolean,
+    saveState: boolean,
+  ): Promise<ShutdownResult> {
+    const results: ShutdownResult = {
+      success: true,
+      shutDown: 0,
+      stateSaved: saveState,
+      errors: [] as string[],
+      duration: 0,
+    };
+
+    const startTime = Date.now();
+
+    try {
+      // Shutdown in reverse order
+      const reverseSequence = [...this.bootSequence].reverse();
+
+      for (const component of reverseSequence) {
+        try {
+          await this.shutdownComponent(component, force);
+          results.shutDown++;
+        } catch (error) {
+          results.errors.push(
+            `${component}: ${error instanceof Error ? error.message : String(error)}`,
+          );
+          if (!force) {
+            results.success = false;
+          }
+        }
+      }
+
+      // Save state if requested
+      if (saveState) {
+        await this.saveShutdownState();
+      }
+    } catch (error) {
+      results.success = false;
+      results.errors.push(
+        `Shutdown error: ${error instanceof Error ? error.message : String(error)}`,
+      );
+    }
+
+    results.duration = Date.now() - startTime;
+    return results;
+  }
+
+  private async shutdownComponent(
+    component: string,
+    force: boolean,
+  ): Promise<void> {
+    // Simplified shutdown logic
+    frameworkLogger.log("mcps/boot-orchestrator", "shutdown-component", "info", { component });
+    // In real implementation, this would properly shut down each component
+    await new Promise((resolve) => setTimeout(resolve, 10));
+  }
+
+  private async saveShutdownState(): Promise<void> {
+    // Save shutdown state
+    const shutdownState = {
+      timestamp: Date.now(),
+      components: Array.from(this.bootStatus.components.keys()),
+      health: Object.fromEntries(this.bootStatus.health),
+    };
+
+    const stateFile = path.join(".opencode", "state", "shutdown-state.json");
+    fs.writeFileSync(stateFile, JSON.stringify(shutdownState, null, 2));
+  }
+
   private formatBootResults(results: BootResults) {
     const response = `🚀 Boot Sequence Results
 
 **Success:** ${results.success ? "✅ COMPLETE" : "❌ FAILED"}
 **Duration:** ${results.duration}ms
-**Components Initialized:** ${results.initializedComponents.length}/${this.orchestrator.bootSequence.length}
+**Components Initialized:** ${results.initializedComponents.length}/${this.bootSequence.length}
 **Components Failed:** ${results.failedComponents.length}
 
 **Initialized Components:**
@@ -365,20 +1057,26 @@ ${results.warnings.length > 0 ? `**Warnings:**\n${results.warnings.map((w: strin
 
     if (detailed) {
       response += `\n\n**Component Details:**`;
-      for (const component of this.orchestrator.bootSequence) {
-        const compHealth = this.orchestrator.getComponentHealth(component);
-        response += `\n• ${component}: ${compHealth ? "✅" : "❌"}`;
+      for (const component of this.bootSequence) {
+        const compStatus = this.bootStatus.health.get(component);
+        response += `\n• ${component}: ${compStatus ? "✅" : "❌"}`;
       }
     }
 
     return response;
   }
+
+  async run() {
+    const transport = new StdioServerTransport();
+    await this.server.connect(transport);
+    frameworkLogger.log("mcps/boot-orchestrator", "start", "success");
+  }
 }
 
 // Start the server if run directly
 if (import.meta.url === `file://${process.argv[1]}`) {
   const server = new XrayBootOrchestratorServer();
-  server.run("boot-orchestrator").catch((error) => frameworkLogger.log("mcps/boot-orchestrator", "run", "error", { error: String(error) }));
+  server.run().catch((error) => frameworkLogger.log("mcps/boot-orchestrator", "run", "error", { error: String(error) }));
 }
 
 export { XrayBootOrchestratorServer };