Added debug directory.
Commandline arguments are now handled by getopt.

process_arguments() now handles this responsibility, and check_args()
has been removed.
Currently, the recursive flag is being implemented.
init_files() was modified in order to assign the correct values.

Small fixes included:
- Many unnecessary comments being removed.
- check_if_dir() didn't check if a target was a file when more than
one source file was specified, which now fails.
- Extra debug features were added.