Think for example, that a user of Universal wants to create a website, but doesn't want to use a database. Or maybe they don't want to use MySQL. The MySQL code should be moved out of UniversalEngine and somewhere else more appropriate. The user should also have the option to use another SQL server of their choosing or not use one at all.
I can most likely do this myself if nobody has a problem with it.
We should delete all files that aren't what we're working on from those 2 branches because it just creates confusion when merging them. For example, delete everything except the modules.php file. Get what I mean?