I've been experiencing a problem with atomic moves in AS5 under Windows. About twice a day, AS5's JVM refuses to release a file handle to META-INF/application.xml or an EJB descriptor file. I cannot swap out the old exploded archive when this happens. This is perplexing since it's not like AS5 is hung. All my apps are still working fine.
In light of this, I would much rather have to touch/copy/delete a marker file than rely on atomic moves.
Also, while I'm sure the HDScanner is performant, the amount of juggling it has to do seems like a convoluted solution for what shouldn't be such a big problem. But then again, if it were that easy, this thread wouldn't even exist.