ruvector 0.2.11 → 0.2.12

package/bin/cli.js

@@ -3551,15 +3551,29 @@ hooksCmd.command('init')
   }
 
   // MCP server configuration (unless --minimal or --no-mcp)
+  // Note: We only use enabledMcpjsonServers (not mcpServers) to avoid
+  // Claude Code regenerating .mcp.json and stripping user-added fields
+  // like autoStart. See: https://github.com/ruvnet/RuVector/issues/250
   if (!opts.minimal && opts.mcp !== false) {
-    settings.mcpServers = settings.mcpServers || {};
-    // Only add if not already configured
-    if (!settings.mcpServers['claude-flow'] && !settings.enabledMcpjsonServers?.includes('claude-flow')) {
-      settings.enabledMcpjsonServers = settings.enabledMcpjsonServers || [];
-      if (!settings.enabledMcpjsonServers.includes('claude-flow')) {
-        settings.enabledMcpjsonServers.push('claude-flow');
+    // Only reference servers via enabledMcpjsonServers — never write mcpServers: {}
+    // which can trigger Claude Code to regenerate .mcp.json
+    const mcpJsonPath = path.join(process.cwd(), '.mcp.json');
+    let mcpJson = {};
+    if (fs.existsSync(mcpJsonPath)) {
+      try { mcpJson = JSON.parse(fs.readFileSync(mcpJsonPath, 'utf-8')); } catch {}
+    }
+    // Only add to enabledMcpjsonServers if the server is defined in .mcp.json
+    if (mcpJson.mcpServers?.['claude-flow'] || mcpJson.mcpServers?.['ruvector']) {
+      const serverName = mcpJson.mcpServers['ruvector'] ? 'ruvector' : 'claude-flow';
+      if (!settings.enabledMcpjsonServers?.includes(serverName)) {
+        settings.enabledMcpjsonServers = settings.enabledMcpjsonServers || [];
+        settings.enabledMcpjsonServers.push(serverName);
       }
     }
+    // Remove stale mcpServers: {} that could trigger .mcp.json regeneration
+    if (settings.mcpServers && Object.keys(settings.mcpServers).length === 0) {
+      delete settings.mcpServers;
+    }
     console.log(chalk.blue('  ✓ MCP servers configured'));
   }
 
@@ -5769,6 +5783,16 @@ hooksCmd.command('doctor')
         };
         Object.values(settings.hooks || {}).forEach(checkCommands);
 
+        // Remove empty mcpServers that can cause .mcp.json overwrites (#250)
+        if (settings.mcpServers && Object.keys(settings.mcpServers).length === 0) {
+          if (opts.fix) {
+            delete settings.mcpServers;
+            fixes.push('Removed empty mcpServers to prevent .mcp.json overwrites');
+          } else {
+            issues.push({ severity: 'warning', message: 'Empty mcpServers in settings.json can cause .mcp.json overwrites', fix: 'Will remove empty mcpServers' });
+          }
+        }
+
         // Save fixes
         if (opts.fix && fixes.length > 0) {
           fs.writeFileSync(settingsPath, JSON.stringify(settings, null, 2));

package/bin/mcp-server.js

@@ -428,7 +428,7 @@ class Intelligence {
 const server = new Server(
   {
     name: 'ruvector',
-    version: '0.2.11',
+    version: '0.2.12',
   },
   {
     capabilities: {
@@ -4132,7 +4132,7 @@ async function main() {
           transport: 'sse',
           sessions: sessions.size,
           tools: 91,
-          version: '0.2.11'
+          version: '0.2.12'
         }));
 
       } else {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ruvector",
-  "version": "0.2.11",
+  "version": "0.2.12",
   "description": "High-performance vector database for Node.js with automatic native/WASM fallback",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",