Ensure proper cleanup during CI stage

[serban-nicusor-toptal]

Submission Checklist

• [ ] Run unit tests
• Documentation
  • [ ] If a user-facing facing change was made, the documentation PR is here:
  • [ ] OR, no user-facing changes were made

Release notes

Because we do not clean after VerifyChanges master is keeping an older state on disk, this PR fixes this behavior.

Copyright and Licensing

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the BSD 3-clause license (https://opensource.org/licenses/BSD-3-Clause)

[serban-nicusor-toptal]

I think this fixed it @WardBrian the problem was that we never cleaned up after Verify Changes so it was keeping the old files there thus an older version of master. I will need to apply this fix to Math, Stan, CmdStan too.

[WardBrian]

@serban-nicusor-toptal the merge on this to master then failed - https://jenkins.flatironinstitute.org/blue/organizations/jenkins/Stan%2FStanc3/detail/master/210/pipeline

Weird, because it seems unrelated to the added rm command?

[serban-nicusor-toptal]

It's because of trying to git diff with origin/{hash} which seems to not work for hashes, I reverted that and we're good!

[WardBrian]

Thanks!