Thread:Manual talk:Skin autodiscovery/Error Message/reply

Modifying Core files is bad and should not be done.

The message in fact is generated in includes/Skin.php, function getSkinNames. Basically there simply is a check for file names of PHP files, which are directly located inside the skins/ folder. Each of these files produces one such warning. Interestingly at least in 1.23, the Core itself still does use autodiscovery while it complains when you do in your skins. That is why there is this funny construct, which filters out Core skins before complaining. Because the Core is still using autodiscovery itself...

However, the solution is to update your skin accordingly. Afterwards the file directly in the folder skins/ is no longer needed and can be removed. With this removal, the warning will disappear.