Add support for filter-repo commit map to cleaner

Git filter-repo is preferred to BFG, but it's output is not identical. Compatibility is added for filter-repo commit map to avoid the need to manually process the commit map before uploading.

Differences between filter-repo and BFG output:

• header included in output by filter-repo
• unchanged commits included in output by filter-repo

This lines can be detected and ignored.

Additionally, this adds refs/pipelines/ to the allow list. This ref was added after the introduction of the cleanup feature

Related to #2832 (closed)