Adding some doc comments

Hey,

I was adding some doc comments. Going through the code, I have fixed a few PSR inconsistency.

Some of the things I noticed are

1 ) PackageXmlParser and 2 ) PackageJsonParser have a different api. 

In one you are expecting a directory path, in the other you expect the .json path. I feel it is worth to change.

Also the gitIgnoreFiles method seems spread, seems some sort of refactoring is good.

Thanks
@harikt 

You have write access. As soon as the doc comment are ready, please apply it :)

Ignore the Installer part, it is a work in progress, should be done until Monday.

@all please check the TODOs too if you like to add features. Except the installer part (I am on it), everything is open :)