One folder to rule them all, One folder to find them,
One folder to bring them all and in the...update...bind them.

Translation: if I want to put the"public_html" folder directly in my HTML folder, it's a little problematic as it has dozens of files and folders directly underneath it (and even more if I have plugins).

It's not a problem if I put geeklog under, say, mydomain.com/geeklog/, but it is when I want to use it directly as mydomain.com

In that case, imagine what it'd be like each time one updates versions! So as not to harm the other files and folders under the HTML folder one would have to delete Geeklog's ones one by one (which is espcially frustrating if done by the supposedly faster SSH instead of by FTP).

If Geeklog would be structured like, say, public_html/files/ (and everything else - except index.php, I guess - would be under "files"), one could have just deleted the "files" folder with a click of a button.

If you use Geeklog directly in yourdomain.com, what do you do to update it easily?

And any chance the "files" approach would be implemented in the future?

Personally, I don't delete, I just overwrite. I might be left with a useless file here or there, but I don't have to worry about knowing what files should or should not be deleted.