fix: STDIO transport stdout flush and MCP notification handling

- Wait for stdout.write callback before process.exit in STDIO transport
  to prevent truncation of large responses (e.g. grafana tools/list)
- Handle MCP notification methods (notifications/initialized, etc.) in
  router instead of returning "Method not found" error
- Use -p shorthand in config claude output

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src/cli/src/commands/config.ts

@@ -98,7 +98,7 @@ export function createConfigCommand(deps?: Partial<ConfigCommandDeps>, apiDeps?:
           mcpServers: {
             [opts.project]: {
               command: 'mcpctl',
-              args: ['mcp', '--project', opts.project],
+              args: ['mcp', '-p', opts.project],
             },
           },
         };

src/cli/tests/commands/claude.test.ts

@@ -45,7 +45,7 @@ describe('config claude', () => {
     const written = JSON.parse(readFileSync(outPath, 'utf-8'));
     expect(written.mcpServers['homeautomation']).toEqual({
       command: 'mcpctl',
-      args: ['mcp', '--project', 'homeautomation'],
+      args: ['mcp', '-p', 'homeautomation'],
     });
     expect(output.join('\n')).toContain('1 server(s)');
   });
@@ -60,7 +60,7 @@ describe('config claude', () => {
     const parsed = JSON.parse(output[0]);
     expect(parsed.mcpServers['myproj']).toEqual({
       command: 'mcpctl',
-      args: ['mcp', '--project', 'myproj'],
+      args: ['mcp', '-p', 'myproj'],
     });
   });
 
@@ -80,7 +80,7 @@ describe('config claude', () => {
     expect(written.mcpServers['existing--server']).toBeDefined();
     expect(written.mcpServers['proj-1']).toEqual({
       command: 'mcpctl',
-      args: ['mcp', '--project', 'proj-1'],
+      args: ['mcp', '-p', 'proj-1'],
     });
     expect(output.join('\n')).toContain('2 server(s)');
   });
@@ -96,7 +96,7 @@ describe('config claude', () => {
     const written = JSON.parse(readFileSync(outPath, 'utf-8'));
     expect(written.mcpServers['proj-1']).toEqual({
       command: 'mcpctl',
-      args: ['mcp', '--project', 'proj-1'],
+      args: ['mcp', '-p', 'proj-1'],
     });
   });
 

src/mcpd/src/services/transport/stdio-client.ts

@@ -61,9 +61,10 @@ proc.stdout.on('data', d => {
       const msg = JSON.parse(line);
       if (msg.id === 2) {
         responded = true;
-        process.stdout.write(JSON.stringify(msg));
-        proc.kill();
-        process.exit(0);
+        process.stdout.write(JSON.stringify(msg), () => {
+          proc.kill();
+          process.exit(0);
+        });
       }
     } catch {}
   }

src/mcplocal/src/router.ts

@@ -367,6 +367,17 @@ export class McpRouter {
       case 'prompts/get':
         return this.routeNamespacedCall(request, 'name', this.promptToServer);
 
+      // Handle MCP notifications (no response expected, but return empty result if called as request)
+      case 'notifications/initialized':
+      case 'notifications/cancelled':
+      case 'notifications/progress':
+      case 'notifications/roots/list_changed':
+        return {
+          jsonrpc: '2.0',
+          id: request.id,
+          result: {},
+        };
+
       default:
         return {
           jsonrpc: '2.0',