Only check md5sum if the file is supposed to be there

This change is in response to an issue that occurred multiple times when deploying [mithril](https://github.com/modcloth-labs/mithril) where a rogue file made its way into the output directory along with the `mithril-server` binary.  The file didn't actually cause any problems per se, but since it was extraneous, it caused the md5sum validation (and therefore the deployment) to fail.  It seems that the original intent of this check is to validate that the files that are supposed to be there are valid, *not* that all of the files present are supposed to be there.

I'm not totally sure if this pull request is a positive change though.  Maybe it is.  Or maybe we should have an additional check that ensures that no rogue files are present (i.e. ensure every file present is in the `MANIFEST` file).  Or maybe we shouldn't merge this pull request because the rogue file was the result of some other issue.  I'm not really sure, so I would love some feedback from other contributors.

For what it's worth, the rogue files were `simple_consumer`, and (iirc) `simple_producer`.  If they were present on just one server, I would have assumed that somebody was testing manually, however, they were present on multiple servers, indicating that they were generated somehow.  Yet, the words `simple`, `consumer`, and `producer` appear nowhere in the `mithril` codebase... :confused: