I swap in and out modules a lot and I see remnants or references to those modules still in my workspace even though the code is no longer there. I made sure to remove them from IntelliJ and went into Windows Explorer and deleted them from the workspace directory. I have even "invalidate cache" from the File menu.
1) When I go to Tomcat Server's deployment tab and add artifacts, I still see a list of EARs/WARs that I no longer care about.
2) This is probably a bug but if I switch compilers, Intellij rebuilds EVERYTHING. It seems to resurrect my old modules and writes them back to my workspace directory (Only the EARs/WARs though).