Jason's fixes (See full comment for changes)

Removed files.php and added it to the .gitignore (poses a vulnerability
otherwise).
Moved the scriptclock js to the assets/ under it's own file, then call
it from the main index.
Moved css and img into their own respective modular housing under
assets/.
Removed redundant comments.
Removed multiple instances of <html> and <head> tags in the scriptclock
(these are redundant if included).
Mmm, indenting. Bitches love indentation.
Moved timetest.php into it's own include/ folder.
Also removed leading slash for files.php. This technically means the /
of the server and can really mess up on some systems. It's best practice
to make this relative when possible.