The only thing that might "break" is if you rely on Webstorm's tools for things like test runners, compiling, minifying and bundling code, etc, instead of learning how to do it on your own. You'd then need to learn how to set it up yourself with the command line tools instead of a nice GUI.
At least use bash/batch files.
I want to be able to build my projects if I ever decide that I don't need it anymore
1. Make an ant/maven/gradle repo, and have the build command run gradle build or something.
2. Create a commandline (open source) tool called "intellibuild" or something, which reads the project files and does whatever the "build" button does.
Unfortunately, they don't do either, so if I don't have a license (or I want to give my code to others who don't use IntelliJ), my J2EE is not buildable.