I don't know if it's relevant, but I use maven and the project files were created using Idea's maven integration. I'm using permanent, not temporary, module files.
Until very recently, the Java EE build settings for my Web facet were working exactly as one would like and in perfect harmony with my maven configuration. I would make sure that in the "Java EE Build Settings" tab of my web facet that I had "Create web module war file " unchecked and that I had "Create web module exploded directory" checked. When I checked the latter the directory that would be automatically inserted into the field below was always something like "/home/mwelch/projects/myproject/target/myproject-webapp". That was exactly right and and worked well with my maven setup.
Well, recently things changed. First, when I clicked the "Create web module exploded directory" the location that was inserted into the field below was "/home/mwelch/projects/myproject/out/myproject-webappWeb". Notice the "out" and the "Web" at the end. This happened on several projects of mine and even deleting all of the Idea project files and starting from scratch did not fix the problem. Second, the deployment just plain 'ole didn't work. When Tomcat would launch, the exploded webapp directory would not be deployed into the container. Nothing I did would cause the exploded app to be deployed. Finally, and I know this is vague and not very useful, things just don't seem to be working right. Even when I manually changed the directory to what it used to be, and the application was being deployed into Tomcat, lots of little things seem to fail on an unpredictable basis. Sometimes classes don't seem to end up in the deployment directory after compilation. Sometimes debugging doesn't work. Lots of little, hard to reproduce things like that.
I know this was long winded, but any ideas about what might be going on here?