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gitaly: Delete log entry after being applied

After a log entry has been applied to the repository, we should ideally delete that entry from the write-ahead log (in our case, the badger database).

Historically we didn't do this, because keeping the entries made it easier to verify database state in the tests.

In this MR we first add mocks over the badger database which also tracks the writes made to the database. Then replace the tests to use the mocks. Finally we delete the log entries after being applied.

Closes #4735 (closed)

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