database: update dbutil-based constructors

Created by: unknwon

Updates a few dbutil-based constructors to accept datbase.DB instead, as they are not mockable in our tests.

Subscribed team please let me know if some dbutil.DBs are on purpose and can break if not using it.

This is the result of a time-boxed effort.

Test plan

Unit tests

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Part of https://github.com/sourcegraph/sourcegraph/issues/26113