Remove QueryRepository, use SQLAlchemy directly

Change-Id: I875df41bb407865e86cf865cbae0c10b775abffe
Remove QueryRevisionRepository

Change-Id: I957048ed6c30eb8db391160277bb4f764dccc3c1
Remove QueryRunRepository

Change-Id: Ib264b11a0ade6137e1d08105a55f627a0049c1a4
Remove UserRepository

Change-Id: I9318b18847b84827eaf1b0be348f2ad23de18d73