This is a nasty side-effect of the old File API usage, which is resolved by using the new Path API.
In some cases we would literally prefix storage paths with a "." directory rather than considering it as conventional interpretation of "current path".
Particularly annoying because "." is our default root directory, I suspect most power users have been setting this to an absolute path but it's confusing for newcomers (and some of our integration tests would do weird things).
I suspect we only have this issue since moving to recent Lucene 4 versions, as we now do some File <-> Path conversions since Lucene moved away from the File API.