Clean up usages of helper.GetRepoPath

GetRepoPath from helper package uses global config.Config variable that makes testing a way lot harder and cause of a race conditions. Now it is marked as Deprecated and should not be used anymore in any new code.
All invocations of it replaced with access to storage.Locator abstraction. The only exception is catfile package that should be slightly refactored to break its dependency on the helper.GetRepoPath.

Part of: #2699 (closed)