fix: correct mcp.json format and Claude Code agent config generation

- Fix getDefaultMcpConfig() in both config-generator.ts and skill-generator.ts
  to use separate command/args fields instead of a single command array,
  which Claude Code requires (resolves issue #235)
- Change ClaudeConfigGenerator to generate .claude/agents/vibe.md (proper
  Claude Code agent config with YAML frontmatter) instead of root CLAUDE.md
- Move Claude Code settings from root settings.json to .claude/settings.json
- Update tests to reflect the corrected output format and file locations

https://claude.ai/code/session_01GHdfjCzUWKxo1CTQibFQ3i

Author: claude

packages/cli/src/config-generator.ts

@@ -130,11 +130,19 @@ abstract class ConfigGenerator {
   protected getDefaultMcpConfig(): object {
     const isWindows = process.platform.startsWith('win');
 
+    if (isWindows) {
+      return {
+        workflows: {
+          command: 'cmd',
+          args: ['/c', 'npx', '@codemcp/workflows-server@latest'],
+        },
+      };
+    }
+
     return {
       workflows: {
-        command: isWindows
-          ? ['cmd', '/c', 'npx', '@codemcp/workflows-server@latest']
-          : ['npx', '@codemcp/workflows-server@latest'],
+        command: 'npx',
+        args: ['@codemcp/workflows-server@latest'],
       },
     };
   }
@@ -215,17 +223,26 @@ class AmazonQConfigGenerator extends ConfigGenerator {
 
 /**
  * Claude Code Configuration Generator
- * Generates multiple files: CLAUDE.md, .mcp.json, settings.json
+ * Generates multiple files: .claude/agents/vibe.md, .mcp.json, .claude/settings.json
  * Merges with existing configuration instead of overwriting
  */
 class ClaudeConfigGenerator extends ConfigGenerator {
   async generate(outputDir: string): Promise<void> {
     const systemPrompt = this.getSystemPrompt();
     const mcpServers = this.getDefaultMcpConfig();
 
-    // Generate CLAUDE.md (system prompt) - always overwrite as it's generated content
-    const claudeMdPath = join(outputDir, 'CLAUDE.md');
-    await this.writeFile(claudeMdPath, systemPrompt);
+    // Generate .claude/agents/vibe.md (agent configuration) - always overwrite as it's generated content
+    const claudeDir = join(outputDir, '.claude');
+    const agentsDir = join(claudeDir, 'agents');
+    await mkdir(agentsDir, { recursive: true });
+    const agentContent = `---
+name: Responsible Vibe
+description: AI assistant that helps users develop software features using structured development workflows.
+---
+
+${systemPrompt}`;
+    const agentPath = join(agentsDir, 'vibe.md');
+    await this.writeFile(agentPath, agentContent);
 
     // Generate .mcp.json (MCP server configuration) - merge with existing
     const mcpConfig: Record<string, unknown> = {
@@ -238,7 +255,7 @@ class ClaudeConfigGenerator extends ConfigGenerator {
     );
     await this.writeFile(mcpJsonPath, JSON.stringify(finalMcpConfig, null, 2));
 
-    // Generate settings.json (permissions and security) - merge with existing
+    // Generate .claude/settings.json (permissions and security) - merge with existing
     const settings: Record<string, unknown> = {
       permissions: {
         allow: [
@@ -254,7 +271,7 @@ class ClaudeConfigGenerator extends ConfigGenerator {
         deny: ['Read(./.env)', 'Read(./.env.*)', 'Read(./secrets/**)'],
       },
     };
-    const settingsPath = join(outputDir, 'settings.json');
+    const settingsPath = join(claudeDir, 'settings.json');
     const finalSettings = await this.mergeWithExistingConfig(
       settingsPath,
       settings

packages/cli/src/skill-generator.ts

@@ -78,11 +78,19 @@ export abstract class SkillGenerator {
   protected getDefaultMcpConfig(): object {
     const isWindows = process.platform.startsWith('win');
 
+    if (isWindows) {
+      return {
+        workflows: {
+          command: 'cmd',
+          args: ['/c', 'npx', '@codemcp/workflows-server@latest'],
+        },
+      };
+    }
+
     return {
       workflows: {
-        command: isWindows
-          ? ['cmd', '/c', 'npx', '@codemcp/workflows-server@latest']
-          : ['npx', '@codemcp/workflows-server@latest'],
+        command: 'npx',
+        args: ['@codemcp/workflows-server@latest'],
       },
     };
   }

packages/cli/test/config-generator.test.ts

@@ -46,20 +46,27 @@ describe('Config Generator', () => {
     it('should generate Claude configuration files', async () => {
       await generateConfig('claude', tempDir);
 
-      // Check CLAUDE.md
-      const claudeMdPath = join(tempDir, 'CLAUDE.md');
-      expect(existsSync(claudeMdPath)).toBe(true);
-      const claudeContent = readFileSync(claudeMdPath, 'utf-8');
-      expect(claudeContent).toContain('whats_next');
+      // Check .claude/agents/vibe.md (agent config)
+      const agentPath = join(tempDir, '.claude', 'agents', 'vibe.md');
+      expect(existsSync(agentPath)).toBe(true);
+      const agentContent = readFileSync(agentPath, 'utf-8');
+      expect(agentContent).toContain('---');
+      expect(agentContent).toContain('name: Responsible Vibe');
+      expect(agentContent).toContain('description:');
+      expect(agentContent).toContain('whats_next');
 
       // Check .mcp.json
       const mcpJsonPath = join(tempDir, '.mcp.json');
       expect(existsSync(mcpJsonPath)).toBe(true);
       const mcpConfig = JSON.parse(readFileSync(mcpJsonPath, 'utf-8'));
       expect(mcpConfig.mcpServers).toBeDefined();
+      expect(mcpConfig.mcpServers['workflows'].command).toBe('npx');
+      expect(mcpConfig.mcpServers['workflows'].args).toContain(
+        '@codemcp/workflows-server@latest'
+      );
 
-      // Check settings.json
-      const settingsPath = join(tempDir, 'settings.json');
+      // Check .claude/settings.json
+      const settingsPath = join(tempDir, '.claude', 'settings.json');
       expect(existsSync(settingsPath)).toBe(true);
       const settings = JSON.parse(readFileSync(settingsPath, 'utf-8'));
       expect(settings.permissions.allow).toContain('MCP(workflows:whats_next)');
@@ -246,8 +253,10 @@ describe('Config Generator', () => {
         expect(mcpConfig.mcpServers['workflows']).toBeDefined();
       });
 
-      it('should merge settings.json with existing permissions', async () => {
-        const settingsPath = join(tempDir, 'settings.json');
+      it('should merge .claude/settings.json with existing permissions', async () => {
+        const claudeDir = join(tempDir, '.claude');
+        mkdirSync(claudeDir, { recursive: true });
+        const settingsPath = join(claudeDir, 'settings.json');
 
         // Create existing settings
         const existingSettings = {

packages/cli/test/skill-generator.test.ts

@@ -94,9 +94,11 @@ describe('Skill Generator', () => {
 
       expect(config.mcpServers).toBeDefined();
       expect(config.mcpServers['workflows']).toBeDefined();
-      // command should be an array
-      expect(Array.isArray(config.mcpServers['workflows'].command)).toBe(true);
-      expect(config.mcpServers['workflows'].command).toContain('npx');
+      // command should be a string, args should be an array
+      expect(config.mcpServers['workflows'].command).toBe('npx');
+      expect(config.mcpServers['workflows'].args).toContain(
+        '@codemcp/workflows-server@latest'
+      );
     });
   });
 
@@ -146,7 +148,7 @@ describe('Skill Generator', () => {
       expect(config.mcp).toBeDefined();
       expect(config.mcp['workflows']).toBeDefined();
       expect(config.mcp['workflows'].type).toBe('local');
-      // command should be an array
+      // OpenCode uses command as array
       expect(Array.isArray(config.mcp['workflows'].command)).toBe(true);
       expect(config.mcp['workflows'].command).toContain('npx');
       expect(config.mcp['workflows'].command).toContain(