I missed one thing yesterday. If you look at the test you can see that the channel is started using the same checkpoint directory later (after checkpoint rebuilder is done rebuilding). This issue with doing that is that the channel will restart with "checkpointDir/checkpoint" as the checkpoint and the new file created by checkpoint rebuilder is ignored. We should probably create the new checkpoint in a different directory and start the file channel with that directory as the checkpoint directory to work around this.
As far as doing the windows specific clean up in a follow up - that sounds ok, but I'd like to make sure that if new directories (as I suggested above) are added to the tests, they get cleaned up when the test is done.