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Move internal files into +gitaly directory

Will Chandler requested to merge wc/counter-skip-quaratine into master

Currently the database and staging directories for the PartitionManager are housed in the root directory of a storage. This may cause the RepositoryCounter to capture staged changes as repositories during startup. In addition, historically Gitaly's internal files for a storage have been kept in the +gitaly directory.

Move the PartitionManager's directories into +gitaly.

Closes #5854 (closed)

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