Project close & plugin shutdown save project-specific preference stores

This addresses [1002304](https://www.assembla.com/spaces/scala-ide/tickets/1002304#/activity/ticket:) :

"The desired Scala installation is not saved when using the project action (right-click on project, `Set Scala Installation`). The project looks ok until restart. The only way the setting is correctly persisted is through the project preferences window."