Move log level defaults into setDefaults

This will allow cliArgs to be only the actual arguments the user passed
which will be used for some logic around opening in existing instances.

src/node/cli.ts

@@ -327,6 +327,21 @@ export const parse = (
 
   logger.debug("parsed command line", field("args", args))
 
+  return args
+}
+
+export async function setDefaults(args: Args): Promise<Args> {
+  args = { ...args }
+
+  if (!args["user-data-dir"]) {
+    await copyOldMacOSDataDir()
+    args["user-data-dir"] = paths.data
+  }
+
+  if (!args["extensions-dir"]) {
+    args["extensions-dir"] = path.join(args["user-data-dir"], "extensions")
+  }
+
   // --verbose takes priority over --log and --log takes priority over the
   // environment variable.
   if (args.verbose) {
@@ -369,21 +384,6 @@ export const parse = (
   return args
 }
 
-export async function setDefaults(args: Args): Promise<Args> {
-  args = { ...args }
-
-  if (!args["user-data-dir"]) {
-    await copyOldMacOSDataDir()
-    args["user-data-dir"] = paths.data
-  }
-
-  if (!args["extensions-dir"]) {
-    args["extensions-dir"] = path.join(args["user-data-dir"], "extensions")
-  }
-
-  return args
-}
-
 async function defaultConfigFile(): Promise<string> {
   return `bind-addr: 127.0.0.1:8080
 auth: password