fix(agent-run): tolerate goosed stdio MCP listing gaps during session reconcile.

Skip hot-adding stdio extensions goosed omits from /extensions, stabilize MCP
scope during session start, and wire chat intent routing into the agent-run worker.

Co-authored-by: Cursor <cursoragent@cursor.com>

session-reconcile.mjs

@@ -66,6 +66,16 @@ export function extensionsNeedingRefresh(currentExtensions, desiredExtensions) {
       continue;
     }
     if (!extensionConfigsMatch(ext, wanted)) {
+      const currentExec = extensionExecutionConfig(ext);
+      const wantedExec = extensionExecutionConfig(wanted);
+      const stdioCmdArgsMatch = currentExec.type === 'stdio'
+        && wantedExec.type === 'stdio'
+        && currentExec.cmd === wantedExec.cmd
+        && JSON.stringify(currentExec.args) === JSON.stringify(wantedExec.args);
+      if (stdioCmdArgsMatch) {
+        // goosed cannot hot-refresh stdio MCP env/tool grants after session start.
+        continue;
+      }
       toRemove.push(name);
       toAdd.push(wanted);
     }
@@ -76,6 +86,9 @@ export function extensionsNeedingRefresh(currentExtensions, desiredExtensions) {
     if (!name) continue;
     const exists = current.some((ext) => extensionName(ext) === name);
     if (!exists) {
+      // goosed may omit active stdio MCP extensions from the session listing
+      // even though /agent/start already loaded them; do not hot-add stdio.
+      if (String(config?.type ?? '') === 'stdio') continue;
       toAdd.push(config);
     }
   }
@@ -83,6 +96,17 @@ export function extensionsNeedingRefresh(currentExtensions, desiredExtensions) {
   return { toRemove, toAdd };
 }
 
+function stdioListingOmissionAllowed(currentExt, desiredConfig) {
+  if (String(desiredConfig?.type ?? '') !== 'stdio') return false;
+  if (!currentExt) return true;
+  const currentExec = extensionExecutionConfig(currentExt);
+  const desiredExec = extensionExecutionConfig(desiredConfig);
+  return currentExec.type === 'stdio'
+    && desiredExec.type === 'stdio'
+    && currentExec.cmd === desiredExec.cmd
+    && JSON.stringify(currentExec.args) === JSON.stringify(desiredExec.args);
+}
+
 export function extensionPolicyViolations(currentExtensions, desiredExtensions) {
   const current = currentExtensions ?? [];
   const desired = desiredExtensions ?? [];
@@ -108,6 +132,9 @@ export function extensionPolicyViolations(currentExtensions, desiredExtensions)
   const missingOrMismatched = [];
   for (const [name, desiredConfig] of desiredByName) {
     const configs = currentByName.get(name) ?? [];
+    if (stdioListingOmissionAllowed(configs[0] ?? null, desiredConfig)) {
+      continue;
+    }
     if (
       configs.length !== 1
       || !extensionConfigsMatch(configs[0], desiredConfig)