Thread:Extension talk:MsUpload/Looking for stuff in /extensions/MsUpload whereas MsUpload is installed in another directory/reply

The fact that you are requiring msupload.php instead of MsUpload.php suggests you are using an old version of the extension. The extension has been heavily updated this last month or so, and the updates include key improvements on the path tracking. I've tried your setup with the latest version and it works. Try downloading the latest version.

However, there will still be a problem: the path to the images won't be resolved correctly, so you won't see the upload button. To solve this, go to MsUpload.php and change where it says  to. This problem seems part of the MediaWiki extension system, not of the extension, so there isn't much else we can do about it.