Yeah, I’ve tried that a couple times with no luck.
Even running the installer, the URL is right. The install folder is right in the base of the site. But once I go to the manager, it starts adding the subfolder to the URL, and it also adds the subfolder to all of my links with Wayfinder and so forth. I put an echo() in config.inc.php, and $base_url is being set to include the subfolder, which means site_url includes the subfolder.
dev_cw, I believe you’re explaining the opposite of what I need.

I don’t want the subfolder to show up anywhere. I have silent rewrites using mod_rewrite to redirect all calls from the root folder to the subfolder. "modx" should never appear in any URL, and all of my base URLs should be just "/".