Krun options

**please review**

* use JCommander for krun
* clean up krun frontend to be more generic
* fix some hacky behavior in some of the options
I don't think those `checkIsFile` calls are correct. Not all backends generate a folder with `definitionName + "-kompiled"` name. (for example, latex and pdf backends).

Another confusing thing is that `checkIsFile` is actually looking for a directory, not a file. So why it's name is`checkIsFile` and not `checkIsDir` ?