Update rule reading and saving, and add option to specify package file.

Removed the translate() methods, they didnt make any sense and they were
actually using an invalid syntax(old version?)

Implemented the --pkg-file argument and with that made modifications to
the PKG_FILE variable to accomodate for the new change.

Added two functions, read_rules() and save_rules() both do as their
names say writing and reading rules from the package file after
detecting what hierachy we are working with.

Updated the directory_to_file() and file_to_directory() functions to use
the new read_rules() and save_rules() functions.