It would be great to have some kind of high-level test but I can't think of it at the moment either.

When it comes to tracking dependencies I made some progress on it in gkossakowski/sbt@abe553671cf054766042775f45c3600f0c8a4d74. I've made dependencies tracking to be SourceFile->ClassName instead of being SourceFile->SourceFile as it's being done now. I'm working finishing it so it becomes ClassName->ClassName (at least for dependencies by inheritance) but this is mostly for experimentation purposes. I don't think I'll be able to merge those patches very soon to sbt (they are rather involved). However, it's still on my roadmap.