Bug 2369 - Add auto-save of workbench model

This patch auto-saves the workbench model so that if Eclipse or the computer it is running on crashes the open editors and workspace arrangement is not lost.

Discussion can be found at: https://bugs.eclipse.org/bugs/show_bug.cgi?id=2369

Aggregation of changes:
- Added a job that auto-saves the workbench.xmi file at a set interval
- Added a preference for changing auto-save interval, can be disabled with 0.
- Added naming and monitor marking to saving jobs.
- Put most of the work in a background job so that the auto-save only takes 0.2 seconds, even on a crappy computer.
- Fixed all bugs involving improperly cleaned model causing duplicate items by cleaning up a copy of the model.
- Removed improper usage of the E4Application object.