Summary:
The file numbers assigned post-repair were sometimes smaller than older files' numbers due to `LogAndApply` saving the wrong next file number in the manifest.

- Mark the highest file seen during repair as used before `LogAndApply` so the correct next file number will be stored.
- Renamed `MarkFileNumberUsedDuringRecovery` to `MarkFileNumberUsed` since now it's used during repair in addition to during recovery
- Added `TEST_Current_Next_FileNo` to expose the next file number for the unit test.
Closes https://github.com/facebook/rocksdb/pull/2988

Differential Revision: D6018083

Pulled By: ajkr

fbshipit-source-id: 3f25cbf74439cb8f16dd12af90b67f9f9f75e718