fix(context): keep MCP protocol output clean

Author: ScriptedAlchemy

.claude-plugin/marketplace.json

@@ -751,7 +751,7 @@ const createContextMcpServer = (
       inputSchema: testSnapshotInput,
       annotations: {
         readOnlyHint: false,
-        destructiveHint: false,
+        destructiveHint: true,
         openWorldHint: true,
       },
     },

packages/context/src/mcp.ts

@@ -1,5 +1,6 @@
 // cspell:ignore modelcontextprotocol
 import path from 'node:path';
+import { Writable } from 'node:stream';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
 import {
   captureLintSnapshot,
@@ -11,6 +12,25 @@ import { withRstackConfigTarget } from './config.ts';
 
 declare const RSTACK_VERSION: string;
 
+const reserveStandardOutputForProtocol = (): Writable => {
+  const standardOutput = process.stdout;
+  const writeProtocol = standardOutput.write.bind(standardOutput);
+
+  Object.defineProperty(standardOutput, 'write', {
+    configurable: true,
+    value: process.stderr.write.bind(process.stderr),
+    writable: true,
+  });
+
+  return new Writable({
+    decodeStrings: false,
+    write(chunk, encoding, callback) {
+      if (writeProtocol(String(chunk), encoding)) callback();
+      else standardOutput.once('drain', callback);
+    },
+  });
+};
+
 const runContextMcpServer = async (startPath: string): Promise<void> => {
   const { workspaceRoot } = await resolveContextWorkspace(startPath);
   const server = createContextMcpServer(workspaceRoot, {
@@ -28,7 +48,7 @@ const runContextMcpServer = async (startPath: string): Promise<void> => {
       }),
   });
 
-  await server.connect(new StdioServerTransport());
+  await server.connect(new StdioServerTransport(process.stdin, reserveStandardOutputForProtocol()));
 };
 
 export { runContextMcpServer };

packages/rstack/src/mcp.ts

@@ -210,7 +210,7 @@ test('registers the exact ordered fifteen-tool catalog with accurate annotations
       });
       expect(tools[12]?.annotations).toMatchObject({
         readOnlyHint: false,
-        destructiveHint: false,
+        destructiveHint: true,
         openWorldHint: true,
       });
       expect(tools[13]).toMatchObject({
@@ -812,6 +812,7 @@ registerHooks({
       name: 'rstack-built-process-test',
       version: '1.0.0',
     });
+    transport.stderr?.on('data', () => undefined);
 
     try {
       await client.connect(transport);
@@ -1691,6 +1692,7 @@ test('loads distinct package lint and test configs through the built root MCP',
       await writeFile(
         path.join(workspaceRoot, fixture.configPath),
         `import { define } from ${JSON.stringify(rstackEntry)};
+console.log('loaded ${fixture.root} config');
 define.lint([{ files: ['src/**/*.ts'], rules: { 'no-debugger': '${fixture.lintRule}' } }]);
 define.test({ include: ['./tests/*.never.ts'], passWithNoTests: ${fixture.testStatus === 'pass'} });
 `,
@@ -1708,6 +1710,14 @@ define.test({ include: ['./tests/*.never.ts'], passWithNoTests: ${fixture.testSt
       name: 'rstack-package-config-test',
       version: '1.0.0',
     });
+    let serverStderr = '';
+    transport.stderr?.on('data', (chunk: Buffer) => {
+      serverStderr += String(chunk);
+    });
+    const transportErrors: Error[] = [];
+    transport.onerror = (error) => {
+      transportErrors.push(error);
+    };
 
     try {
       await client.connect(transport);
@@ -1743,6 +1753,9 @@ define.test({ include: ['./tests/*.never.ts'], passWithNoTests: ${fixture.testSt
       for (const result of [...lintResults, ...testResults]) {
         expect(result.isError).not.toBe(true);
       }
+      expect(transportErrors).toEqual([]);
+      expect(serverStderr).toContain('loaded packages/app config');
+      expect(serverStderr).toContain('loaded packages/library config');
 
       expect(lintResults.map((result) => result.structuredContent)).toEqual([
         expect.objectContaining({