Fixes #414 NPE during launch
If you used version=project in the -runbundles
then it installed the bin directory as a bundle. This normally has no
manifest, and it is against the idea that we always build bundles. So
we generate a warning. It also likely fails on Windows since we cannot
use the reference:.

It is a warning because I am not sure if anybody uses this feature. There
could be some use cases.

Additionally, the XML JUnit reporter is changed so that even if you put
a directory as a bundle, you do not get the NPE anymore