“intelligently” parsing user input arguments<>
This question already has an answer here:
Use Apache Common CLI library. It can parse options and arguments very well. http://commons.apache.org/proper/commons-cli/
There are numerous Java libraries "out there" that can help you with command line parsing; see Is there a good command line argument parser for Java? for examples.
However, parsing command arguments "intelligently" depends on where you are coming from:
If you want something that will parse command arguments according to a consistent syntax or meta-syntax, then some of those examples will surely do that.
If you want something that will magically understand what the user really means, then you are dreaming