Add shared port registry workflow and improve scaffold tooling

install/merge-managed-mcp-config.mjs

@@ -205,6 +205,16 @@ function parseJsonc(input, label) {
 }
 
 function parseJsoncAst(input, label) {
+  if (!input.trim()) {
+    return {
+      type: "object",
+      start: 0,
+      end: 0,
+      properties: [],
+      value: {},
+    };
+  }
+
   let index = 0;
 
   function fail(message) {
@@ -780,9 +790,10 @@ function main() {
   const allManagedServerNames = new Set(Object.keys(managedConfig[options.serverKey]));
   const desiredServerNames = new Set(Object.keys(managedServers));
 
-  const targetText = fs.existsSync(options.target)
+  const existingTargetText = fs.existsSync(options.target)
     ? fs.readFileSync(options.target, "utf8")
-    : "{}\n";
+    : "";
+  const targetText = existingTargetText.trim() ? existingTargetText : "{}\n";
   const targetAst = parseJsoncAst(targetText, options.target);
   const cleanedTargetText = removeStaleManagedServers(
     targetText,