Fixed a couple issues with loading different simulation files.

If there is a simulation file already loaded, loading another simulation file will cause the model entites not showing up in the attribute-entity association window. Also, it will crash in certain cases where model manager is directly used in attribute system to query entities. The bug is that when loading a different file, the application would clear current attribute system, and create a new attribute system, but did not set the model manager to the new attribute system, hence the issues.