It would be nice if you could do automatic project update(maybe an option in project context menu) if there are changes in local file system.
1. When I recreate project I want to add my previous soql and anonymus code files to project just by moving them to \AnonymousApex and \Soql folders.
2. When *.cls file is created in folder add it to project. And when file is missing in folder remove it from project or maybe even try to remove it from Salesforce.