Revert "Make VisibleRefFilter.Filter reuse the refs passed from JGit."

This reverts commit b032a529f83892dfbdfb375c47a90d89756dd8ab. This
commit introduced an issue where tags were not replicated under certain
circumstances.

Bug: Issue 2500
Bug: Issue 1748
Change-Id: I9c902b99c7f656c7002cf3eab9e525f22a22fb85
Merge "Revert "Make VisibleRefFilter.Filter reuse the refs passed from JGit."" into stable-2.9