Separate modules in submission artifact

[alexstaeding]

Currently, the submission archive is created by flattening all modules and source sets into a single source zip/jar. While this works well for single-module projects, it is not optimal for multiple modules.

This PR is part of a larger effort to make Jagr more module-aware. The first step is to split up modules in the submission archive similarly to the way modules are split up in subfolders during development. Modules are significantly more logically separate units than source sets (e.g. different classpath, dependencies etc...) so it makes sense to split them up into subfolders for the submission.

For now, source sets will continue to be flattened into one module output.