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Set HEAD from backup bundle files

James Fargher requested to merge backup_update_head into master

Fixes #3856 (closed)

Previously backup relied on git-clone setting HEAD from bundle files but now that we apply a series of bundles, the bundles are applied using git-fetch instead. This means we need to apply our own HEAD setting logic based off of the bundle.

ChecksumTestRepo was incorrectly calculating repository checksums without HEAD.

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