feat(cli): report opt-in command timings (#7042)

* feat(cli): report opt-in command timings

* fix(cli): time standalone MCP doctor

* fix(cli): retain timing on doctor errors

* fix(cli): preserve formatted version output with command timings

---------

Co-authored-by: dhruvac29 <dhruvac29@users.noreply.github.com>
Co-authored-by: gensokyo-dev <342580529+gensokyo-dev@users.noreply.github.com>

scripts/rea.mjs

@@ -68,15 +68,34 @@ if (!(await compiledRuntimeExists(runtimeFiles))) {
   await runMcpHttpEntrypoint(args.slice(1));
 } else if (isMcpDoctorMode) {
   guardClosedStdout();
-  const { runProductionMcpDoctorCli } =
-    await import("../dist/cli-runtime/mcpDoctor.js");
-  const result = await runProductionMcpDoctorCli(doctorArguments, {
-    dispatcherPath: fileURLToPath(import.meta.url),
-    packageRoot,
-    stdoutIsTerminal: process.stdout.isTTY === true,
-  });
-  writeStdout(result.output);
-  process.exitCode = result.exitCode;
+  // Doctor runs outside Incur, so handle its global timing flag here. Keep a
+  // token consumed by --format as a value, even when it looks like a flag.
+  const outputValues = new Set(
+    builtinArguments
+      .splitIncurBuiltinArguments(doctorArguments)
+      .outputValues.map(({ index }) => index),
+  );
+  const doctorCliArguments = doctorArguments.filter(
+    (argument, index) => argument !== "--timings" || outputValues.has(index),
+  );
+  const timingRequested = doctorCliArguments.length !== doctorArguments.length;
+  const started = performance.now();
+  try {
+    const { runProductionMcpDoctorCli } =
+      await import("../dist/cli-runtime/mcpDoctor.js");
+    const result = await runProductionMcpDoctorCli(doctorCliArguments, {
+      dispatcherPath: fileURLToPath(import.meta.url),
+      packageRoot,
+      stdoutIsTerminal: process.stdout.isTTY === true,
+    });
+    writeStdout(result.output);
+    process.exitCode = result.exitCode;
+  } finally {
+    if (timingRequested)
+      process.stderr.write(
+        `${JSON.stringify({ rea_timings: { version: 1, command_ms: Math.round(performance.now() - started) } })}\n`,
+      );
+  }
 } else {
   const {
     cliConfigurationError,