OK, I'll look into copying appropriate bits of the essay question type into CodeRunner to allow file upload, but I'll do this only in the development branch for a start, as I'm still not sure where it's going.
Tim's question of how to deal with the files is a good one. My assumption is that any files attached to the student submission should just be copied into the working directory before the template-generated code is run. But then what?
The easiest approach from a developer's standpoint, as it doesn't require any extended functionality, is to use the template code as a control script, probably written in Python. It could just list the working directory to see what was uploaded and then take whatever action was necessary, e.g. unzipping a .zip attachment or compiling a Java program with a -jar <upload.jar> command line parameter.
For extra flexibility I could add a template parameter FILE_NAMES, which contains the names of all uploaded files. One could then deal with uploaded files at the Twig level rather than at the template_scripting level. However you're limited in what you can do there, e.g., you can't add command line options for compiling. So I'm not sure that having the FILE_NAMES variable really helps much and it might just confuse inexperienced authors. Mostly you're going to have to fire the job off to Jobe for execution anyway, so dealing with the files there, in a much more powerful language, would usually be my preferred approach. Nowadays virtually all our advanced question types are written as Python scripts.
Thoughts, anyone? Particularly, Trent - what did you have in mind?
BTW: don't expect any lightning action on this - our second semester is about to start and I don't usually feel like playing with CodeRunner development while I'm teaching.