Improved logic; support in-flight manifests in separate git-controlled directory

Change-Id: I6cd7f8df5ea05540ce1daf81547acf67f347794b
Reviewed-on: http://review.couchbase.org/33052
Reviewed-by: Chris Hillery <ceej@couchbase.com>
Tested-by: Chris Hillery <ceej@couchbase.com>