add unified interface for accessing file system

**please review**
Can you make an issue for me on this one? You have made a very good suggestion here, but I'd like to do it in a separate pull request to keep this one cleaner. It's a bit of an involved change which affects parts of the code this diff doesn't have to modify. All this is really doing is copy-pasting code already present in KRunModule into JavaSymbolicKRunModule.