For awhile we've supported automatic detection guessing if the webserver supports PATH_INFO and if so automatically using /index.php/$1 for the article path. I believe this even predates our better REQUEST_URI handling.
I'm considering the idea of dropping support for this automatic setup.
[..]
I don't really like the idea of dropping it, unless our detection of it not working really does suck. Moving servers is going to break things no matter what. This is especially true now that $wgServer is set explicitly instead of auto-detected.
If we're worried about auto-detection failing, we could do better auto-detection in the install script ( Make an ajax request to some script /mw-config/path_info.php/test and see if it can properly extract the path info).
-bawolff