Another solution to this problem would be to get rid of the internal repository, and resolve the inter-project artifacts directly from the build dir.

You probably know this already. To clean the internal repository you can do the -C rebuild. Removing it by clean might be a better way of doing things, but I'm not sure. Let's say you only want to build a particular subproject. You want to do this with a clean. Do you want a rebuild of all the projects its depends on? I agree with Adam that getting rid to the internal repository all together would be nice. But this would give us basically the same behavior as we have now. For partial builds a clean would only clean the subproject. For a full build we upload the newest versions to the internal repository anyway.

I like Adam's solution better too. My goal was that if I ran a clean on a particular subproject, it's artifact(s) would be removed from the internal repository.

We had an issue where different developers with identical source were getting different test resuls after a clean build. Removing the internal repository fixed the issue (which I still don't understand), but I didn't feel that this should have been necessary.

Internal repository no longer exists, so this should fix this problem