Fix issue 47. and 48 Actually use all the files.... and dont run over deleted ones

[Bachmann1234]

This one was embarrassing. I suspect I broke it during the grand refactoring a while back.

Here is the original issue:
#47

I am going to look at issue48 before merging this. Maybe combine them as one release.

[coveralls]

Coverage decreased (-0.2%) to 98.797% when pulling decbf17 on issue-47 into 0c593e8 on master.

[coveralls]

Coverage increased (+0.0009%) to 99.038% when pulling 85a7349 on issue-47 into 0c593e8 on master.

[coveralls]

Coverage increased (+0.01%) to 99.049% when pulling 552bfe4 on issue-47 into 0c593e8 on master.

[fperrin]

Hi Matt,
Same comment, new version of diff-cover does fix the issue I was seeing in our repo, so looks good to me. Thanks for the fix!