The <file> parameter should be the path to the "My Clippings.txt" file.
e.g. "java -jar ClippingsExtractor.jar /home/My\ Clippings.txt"
As this was just an initial proof of concept to show what the library could do I didn't add the code to handle all the exceptions correctly and instead just printed a stack trace which is what you relieved when you didn't enter the file path.
Future versions will handle things better. This version was written over a couple of days in a short period of time after work each day and as such is not as complete as it could be.