I have a large project which consists of two modules. One contains a web facet, and the other is just a pure java module. Within the web facet module I then added the pure java module as a dependency, and also within the web facet module I've enabled the option to "create web facet exploded directory." So, then when I run a "Ctrl-F9 (Make)" I get all of the compiled classes from either module copied into the "WEB-INF/classes" directory within the exploded directory. That all works fine.
If I then go to edit a file within the pure java module and I use "Ctrl-Shift-F9 (Compile Class)" the class file does get compiled and created in my project's compiler output directory. However, it does not get automatically also copied into the "WEB-INF/classes" directory within the exploded directory. Then, the next time I run a "Ctrl-F9 (Make)", Idea appears to think that things have gotten out of sync, so it re-copies all of the classes from the compiler output directory into the exploded directory. In my project there are thousands of class files, so this re-copy process takes a painfully long time.
I recently upgraded to Idea 8 from Idea 6, and I didn't have this problem in the previous version. (I never used Idea 7 though, so not sure if it was an issue there or not.)
I'm attaching a zip file with my ipr / iml files in case it's of use.
Environment: Windows XP
Issue was resolved