Fix changed file detection on Travis (GH-3129)

Travis when merging changes from a pull request onto the target branch
does not perform a rebase, instead it does a simple merge which causes
the PR commits to retain their commit dates. This means that the commit
log can potentially look like:

PR merge <-- HEAD
normal master commit <- master
more commits from normal workflow
PR commit 1
another master commit
PR commit 2

Performing a git diff from PR commit 2 to master will accidentally
include files that should not be there.

Closes python/core-workflow#14