Previously, when we run `rake build` in a non-base branch it will be
run at the Git state before the base branch merge, resulting in mixed
Git state. And since the merge happens in auto/build it will obviously
also be run in an pre-merge state. This can cause all sorts of subtle
build errors.

So let's move this merge earlier, into the Rakefile, so only changes
there can be mixed. Also, this builds a foundation for completely
eliminating this mixed state (soon!).