When some test was creating an element and then removing it, it would also remove user and application as they wasn't used anywhere else.
`ifcopenshell.util.element.remove_deep2(file, history)` we use in every api for element deletion can possibly remove user and application which can be unsafe if `get_user` is returning some specific entity that then will become invalid.
Also fixed tests breaking due ifcownerhistory and user/application appearing in ifc2x3.
it was creating new applications and users every time `ifcopenshell.api.owner.settings.get_user` or `ifcopenshell.api.owner.settings.get_application` was called
Dion Moult