While the GUI is great, I would appreciate getting more mileage out of the XML configuration files. Particularly, I would rather create/modify run configurations directly in the .iws file. One reason for this is that for some of us, the features we want to change are much easier to find this way, and it simplifies cloning and modifying settings.
I notice that when I do this from within IDEA, the changes I make in the editor are immediately overwritten, say on a Ctl-S.
It seems IDEA should either lock the file (at least from within its own editor), or reload the .iws settings. I would rather not have to quit the IDE to make these changes in text.