Before doing any mods, the recommended procedure is to back up your current store. But what I did was to copy the entirety of the "store" folder to "store1". I made a few changes to some files in the "store1" version, nothing serious, then swapped the folder names: "store" to "store-orig", and "store1" to "store".

But now the script (includes/content/index.inc.php) cannot find "language/en/home.inc.php". It's there and has 644 permissions. It also cannot find "classes/cart.php", but it's there and has 644 permissions.

What could copying a root-level folder to a copy of itself, then renaming the copy to the original folder name cause this kind of problem?

Might it have something to do with any kind of server-based code optimizer or server-level cache system?