baseDir as array and added output wrapper

I have changed a bit of the code and added some features.

 - the `baseDir` parameter can now be either a string or an array of strings.
 - added `wrapper` parameter which allows you to wrap your code.
 - changed the behavior of the paths. everything now is relative to the directory of the JSON. This is something useful if you have 5 projects, each one with it's own configuration JSON.

P.S. I hope i haven't messed up the code too much, because my Eclipse is not yet set to auto-format the JAVA files as it should and also because i haven't used git to actually clone the repository and work locally. 

P.P.S. Please also make an executable jar with each pull in master, because the current jar still has that issue of having path resolution problems, and i could say that this is the reason i forked the project ( i mean until now i hadn't even had a github account :smile:  )