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it looks like you have version 2.2.x (a somewhat deprecated release), the current stable version (2.0.16) does not have these files (it has a different file as specified release notes in the archive)
the login popup option (as I see from opening the script file) specifies that it is for logins using ssl, so unless you have that, you can't really use it. Anything in the 'extras' folder would need to be uploaded to wherever it should go. For example, the login.php script says this:
Quote:
This script displays a login screen in a popupbox when SSL is enabled in the preferences. You should use this script only when your server supports SSL. Place this file under your SSL directory
If a module contains and 'extras' folder inside it, most likely it should stay right where it is (inside the module's folder) but definitely read its documantation to make sure.
As for the theme files, it may be good for experimentation and testing, but you can format your news into 2 or more columns using the latest news module without any mods I believe.
So imo, if you really wish to use XOOPS 2.2.x, I would ignore the extras folder altogether