Warning on bare filename w/ directoryPrefix

Prints a warning to the terminal if the plug-in encounters a bare
filename partial in a ruleset that has specified a directoryPrefix.
Update README for new options

Adds directoryPrefix and filenamePrefix to the options list, replacing
the old prefix option.
Rename new options to use underscores

Switches directoryPrefix to prefix_dir and filenamePrefix to
prefix_file, which more closely matches the existing naming convention
used by the other options. By renaming directoryPrefix, this also avoids
the inherent confusion with the unrelated 'directory' option.