You can clone with
In my workflow of running Jekyll then using Transmit.app's "Sync by timestamp" ... it would be really nice if there were a _config.yml setting that said "when generating files in the _site directory, preserve the file timestamps" so that files that files in the _site directory don't all keep getting touched with the current timestamp and thus causing the sync process to copy all the files every time even when their contents haven't changed.
That would be cool, but it would dramatically increase compile time. We'd have to check against both the modification time of the post/page and of the layout it is placed in.
Not sure this is going to change. We have to regenerate the entire site every time something has changed (we don't know dependencies) and checking if the file contents have changed. This isn't really a viable option for the project in my opinion and I think @mojombo would agree.