I found a similar problem buried in a thread somewhere else but I thought I'd start a new thread on this since it seems to stand on it's own.
Ever since IDEA changed to require a WebModule as a separate module, the Check In Project command has been ignoring all the JSPs and other web files in the Web Project.
Everything else works fine, I can check them out, check them in individually, etc. But they don't show up in the list of files to check in for the whole project.
I've tried adding a "source" folder to the web module at the top of it to no effect.