A problem with the new build from the source code reorg is that you can't or at least shouldn't run clean together with other targets on the same command line. Also the reconfigure target is not compatible with running with other targets.

I have figure out a way to fix this. In the top Makefile, which is still run sequentially, we can filter out the targets needing special attention (clean and reconfigure) and run those by themselves in sequence. Clean and reconfigure typically needs to be run before the rest of the targets. With this assumption we can easily serialize execution in that order.