Started documentation

I've started to read this code and as I figure out what it's doing I
document it. I may have (will) tweek it a bit here and there.
Documentation Cont'd

Added documentation to the properties nav_{dir,point}, the constructor,
check_config, remove_ignore, and get_files methods.

Changed the parameter name from dir to dir_contents in remove_hidden
method.
Finished Changing Param/Variable Name

I had changed the parameter name for the function remove_hidden from $dir to
$dir_contents in an effort to make the name more descriptive, but I
didn't change the name everywhere in the function; I fixed that error.