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praefect: Add -db-only flag to remove repository

Will Chandler requested to merge wc-remove-db-only into master

In some situations, most notably Geo replication, a large number of repos may be present in the DB but not on disk. It's possible to remove these entries using the remove-repository sub-command, but this creates a risk of accidentally deleting a repo that's present on disk and triggering permanent dataloss.

This MR adds a new -db-only flag to remove-repository allowing admins to be confident that even if an on-disk repo is passed in it won't be deleted from disk and can be re-tracked easily.

Closes #4279 (closed)

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