This is an excerpt from a conversation trying to fix a student project where there was a wordpress site in the home directory and someone installed Omeka over top of it, then when Wordpress auto updated it overwrote the index.php file and rendered the Omeka site useless.
The trick is once we know that is fully correct you can blow away everything in the main directory, and clone the bk.hussa100 back over to the main directory. There is another omeka install in there that is called omekadelete that can be deleted as well
So the fix (which I'm going to document in my known site) is that I cloned the Omeka instance off to a subdomain, but when I did that it took the files that were changed by wordpress yesterday... The key file that was screwing everything up will not be surprising, it was index.php. So I installed a new version of Omeka and copied the index.php file from there over to the bk.hussa100 site.
Moral of the story... we now know that when you install wordpress over Omeka in a directory, that the index.php file appears to be the only one that is overwritten by WP. Because the Omeka Classic index.php is not different from one Omeka instance to another any copy of an Omeka Classic index.php would work (so in theory I could have grabbed it from their github as well)