Allow including unreachable objects in transaction

Some RPCs in Gitaly, such as UserSquash, write objects into the repository without making them reachable. The TransactionManager only includes objects in the logged pack file that are reachable. This creates a problem for those RPCs as the objects they attempt to write do not get committed into the repository. This commit enables committing unreachable objects in a transaction. The problematic RPCs can include specific objects in the pack even if they are not reachable from the references so they get committed as part of the transaction.

Closes #5451 (closed)