Replace `Repo.get(Module, id)` with `Module.get_by_id(id)` where possible

This MR:

• Replaces Repo.get(Activity, id) => Activity.get_by_id(id)
• Replaces Repo.get(User, id) => User.get_by_id(id)
• Does not add Activity.get_by_id/1 and User.get_by_id/1, they exist for quite awhile.