use File instead of String

I know that the compiler is still in development; however I tried to run the compiler in my Ubuntu development machine and it failed because all paths are Windows specific. 

I replaced `"\\"` with `File.separator` and tried to use the `new File(File parent, String child)` constructor if the parent folder is already present or used multiple times. On longer paths I used `String.replace` to maintain readability.

I replaced `for(String x : f.list())` with `for(File x : f.listFiles())` for consistency, however the previous solution with Strings was not causing any trouble.

There are a lot of `File` constructions from paths provided in the options, I think it would be better to use `File` instead of `String` already there but I didn't want to change too much.