In web module it is possible to check option to build war files. But building war files especially when you has a lot of libraries takes a lot of time so when I am coding/running my application I turning off this option but when I need to deploy it I turn it on again and build war files, deploy it and turn off again.
May be it will be better if you will remove this option from web module settings and create module specific action in project view etc to build war file?