fix: Claude Desktop MCP JSON parsing errors after July 23, 2025 breaking change

index.ts

@@ -34,8 +34,8 @@ class CodeContextServer {
 
     this.setupToolHandlers();
 
-    // Error handling
-    this.server.onerror = (error) => console.error("[MCP Error]", error);
+    // Error handling - comment out to avoid JSON parsing conflicts
+    // this.server.onerror = (error) => console.error("[MCP Error]", error);
     process.on("SIGINT", async () => {
       await this.server.close();
       process.exit(0);
@@ -47,7 +47,7 @@ class CodeContextServer {
       tools: [
         {
           name: ToolName.QUERY_REPO,
-          description: "Queries a git repository using semantic and keyword search. Use keywords and file patterns if you want to targer specific files or terms",
+          description: "Queries a git repository using semantic and keyword search. Use keywords and file patterns if you want to target specific files or terms",
           inputSchema: zodToJsonSchema(QueryRepoSchema),
         },
       ],
@@ -94,7 +94,7 @@ class CodeContextServer {
               ],
             };
           } catch (error) {
-            console.error("Error in query_repo:", error);
+            // console.error("Error in query_repo:", error);
             return {
               content: [
                 {
@@ -113,9 +113,12 @@ class CodeContextServer {
   async run() {
     const transport = new StdioServerTransport();
     await this.server.connect(transport);
-    console.error("Code Context MCP server running on stdio");
+    // console.error("Code Context MCP server running on stdio");
   }
 }
 
 const server = new CodeContextServer();
-server.run().catch(console.error);
+server.run().catch((_error) => {
+  // Silent error handling to avoid JSON parsing conflicts
+  process.exit(1);
+});

start.ts

@@ -17,17 +17,19 @@ const NODE_ENV = process.env.NODE_ENV || 'development';
   }
 });
 
-process.stderr.write(`Starting Code Context MCP Server\n`);
-process.stderr.write(`Data Directory: ${DATA_DIR}\n`);
-process.stderr.write(`Repo Config: ${REPO_CONFIG_DIR}\n`);
-process.stderr.write(`Node Environment: ${NODE_ENV}\n\n`);
+// Log to a file instead of stderr to avoid JSON parsing conflicts
+// Uncomment these lines if you need debug output, but redirect to a log file
+// process.stderr.write(`Starting Code Context MCP Server\n`);
+// process.stderr.write(`Data Directory: ${DATA_DIR}\n`);
+// process.stderr.write(`Repo Config: ${REPO_CONFIG_DIR}\n`);
+// process.stderr.write(`Node Environment: ${NODE_ENV}\n\n`);
 
 const checkOllama = () => {
   try {
     const result = spawn('pgrep', ['ollama'], { stdio: 'pipe' });
     result.on('exit', (code) => {
       if (code !== 0) {
-        process.stderr.write('Starting Ollama...\n');
+        // process.stderr.write('Starting Ollama...\n');
         spawn('ollama', ['serve'], { detached: true, stdio: 'ignore' }).unref();
         setTimeout(() => startMcpServer(), 3000);
       } else {

wrapper.ts

@@ -0,0 +1,30 @@
+#!/usr/bin/env node
+
+import {writeFileSync, appendFileSync} from 'fs';
+
+const LOG_FILE = process.env.LOG_FILE || '/tmp/mcp-code-context.log';
+
+const safeLog = (level: string, ...args: any[]) => {
+    if (!LOG_FILE) return;
+    try {
+        appendFileSync(LOG_FILE, `[${level}] ${new Date().toISOString()} ${args.join(' ')}\n`);
+    } catch (e) {
+    }
+};
+
+const createLogger = (level: string) => (...args: any[]) => safeLog(level, ...args);
+
+console.log = createLogger('LOG');
+console.error = createLogger('ERROR');
+console.warn = console.info = console.debug = console.log;
+
+try {
+    writeFileSync(LOG_FILE, `[INIT] ${new Date().toISOString()} Code Context MCP Server starting\n`);
+} catch (e) {
+}
+
+import('./index.js').then(() => {
+}).catch(error => {
+    safeLog('FATAL', error);
+    process.exit(1);
+});