fix: read MCP servers from both ~/.claude.json and ~/.claude/settings.json

Claude CLI stores user-scoped MCP servers in ~/.claude.json, while
CodePilot was only reading from ~/.claude/settings.json. Now both
the MCP list API and streamClaude merge configs from both sources.

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

src/app/api/plugins/mcp/route.ts

@@ -13,16 +13,24 @@ function getSettingsPath(): string {
   return path.join(os.homedir(), '.claude', 'settings.json');
 }
 
-function readSettings(): Record<string, unknown> {
-  const settingsPath = getSettingsPath();
-  if (!fs.existsSync(settingsPath)) return {};
+// ~/.claude.json — Claude CLI stores user-scoped MCP servers here
+function getUserConfigPath(): string {
+  return path.join(os.homedir(), '.claude.json');
+}
+
+function readJsonFile(filePath: string): Record<string, unknown> {
+  if (!fs.existsSync(filePath)) return {};
   try {
-    return JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
+    return JSON.parse(fs.readFileSync(filePath, 'utf-8'));
   } catch {
     return {};
   }
 }
 
+function readSettings(): Record<string, unknown> {
+  return readJsonFile(getSettingsPath());
+}
+
 function writeSettings(settings: Record<string, unknown>): void {
   const settingsPath = getSettingsPath();
   const dir = path.dirname(settingsPath);
@@ -35,7 +43,12 @@ function writeSettings(settings: Record<string, unknown>): void {
 export async function GET(): Promise<NextResponse<MCPConfigResponse | ErrorResponse>> {
   try {
     const settings = readSettings();
-    const mcpServers = (settings.mcpServers || {}) as Record<string, MCPServerConfig>;
+    const userConfig = readJsonFile(getUserConfigPath());
+    // Merge: ~/.claude/settings.json takes precedence over ~/.claude.json
+    const mcpServers = {
+      ...((userConfig.mcpServers || {}) as Record<string, MCPServerConfig>),
+      ...((settings.mcpServers || {}) as Record<string, MCPServerConfig>),
+    };
     return NextResponse.json({ mcpServers });
   } catch (error) {
     return NextResponse.json(

src/lib/claude-client.ts

@@ -283,8 +283,28 @@ export function streamClaude(options: ClaudeStreamOptions): ReadableStream<strin
           };
         }
 
-        if (mcpServers && Object.keys(mcpServers).length > 0) {
-          queryOptions.mcpServers = toSdkMcpConfig(mcpServers);
+        // Load MCP servers: use passed-in config, or auto-read from config files
+        let effectiveMcpServers = mcpServers;
+        if (!effectiveMcpServers || Object.keys(effectiveMcpServers).length === 0) {
+          try {
+            const userConfigPath = path.join(os.homedir(), '.claude.json');
+            const settingsPath = path.join(os.homedir(), '.claude', 'settings.json');
+            let merged: Record<string, MCPServerConfig> = {};
+            if (fs.existsSync(userConfigPath)) {
+              const userConfig = JSON.parse(fs.readFileSync(userConfigPath, 'utf-8'));
+              if (userConfig.mcpServers) merged = { ...merged, ...userConfig.mcpServers };
+            }
+            if (fs.existsSync(settingsPath)) {
+              const settings = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
+              if (settings.mcpServers) merged = { ...merged, ...settings.mcpServers };
+            }
+            if (Object.keys(merged).length > 0) effectiveMcpServers = merged;
+          } catch {
+            // ignore config read errors
+          }
+        }
+        if (effectiveMcpServers && Object.keys(effectiveMcpServers).length > 0) {
+          queryOptions.mcpServers = toSdkMcpConfig(effectiveMcpServers);
         }
 
         // Resume session if we have an SDK session ID from a previous conversation turn