Having the idea project files all within the idea/ directory is a bit of a pain. The natural location for these would be in the .idea directory on the top level. This would mean that a person wanting to use IDEA to work with JavaFX would open the "rt" directory directly instead of the "rt/idea" directory. It also means that from IDEA, if you were to clone a new workspace and clone the rt directory, it would be able to find the .idea directory and recognize that you have cloned an IDEA project and open it immediately. .idea is the normal name idea uses for project based directories, and should be at the top level of the project.