Deprecate git_data_dirs in Omnibus for Gitaly for removal in 17.0

Omnibus currently has multiple ways of configuring Gitaly storages:

• The preferred method of setting gitaly[:configuration][:storage]
• Legacy method of configuring git_data_dirs

Ideally we'd only have one way to configure storages, and preferably that would be by configuring them directly for Gitaly.

There's also some complex back and forth logic. Configuring repository storages in Rails automatically from Gitaly's storages may make sense, but there's also logic to configure Gitaly's storages from Rails. This doesn't seemingly make much sense given Rails should not know the storage paths. We may want to remove this logic.