Committing files that don't have changes apparently.
Merge remote-tracking branch 'origin/dev' into mullins

Conflicts:
	Application.e4xmi
Added the LifeCycleManager for early initialization of some of our
managers; no longer setting managers up from within Parts.
Implemented workaround for Eclipse's Persisted State bug: manually load
the data from the workbench.xmi file before the application model is
loaded then add it to the Persisted State after it gets loaded.
Added parameter to the removeProject command to specify the name of the
Project to be removed.
Added ConfirmWithOptionDialog and ability to delete Project contents on
disk.
Fixed race condition in ImportFileWizard and added multi-select to
ImportFileWizardChooseFilesPage.
Fixed SettingsPart injection issue by reworking selection notification
so it only sees the selection for the DataEditorPart.
Fixed small issues in QuickAnalysisPart
added to BasicMainPart
Merge remote-tracking branch 'origin/mullins' into maresca_merged
merge with mullins branch, updates to BasicMainPart
Merge remote-tracking branch 'origin/dimou' into maresca_merged
updated instantiated objects in LifeCycleManager, updated Software
Manager to detect actual plugins, updated Basic Main Part with tab
reformatting, and added contents for visualization tab