* Added logging with SLF4J and Logback
* Added `--version` option.
* Mofidied the input file rules. When an input object is a directory, JLPMain is
adding all the files in that directory and its subdirectories. Now JLPMain is
ignoring hidden files in the directory and subdirs. A file named explicitly on
the command line is still included regardless of if it is hidden or not.
* Documentation continues.