TL;DR: Import as a Non-BlueJ project to run in BlueJ.
When dealing with Java projects containing subfolders, BlueJ creates unique package.bluej for every single subfolder. This can be a hassle with multi-folder projects. Importing as a non-BlueJ project is easier than having Git store a new BlueJ file for every empty folder.
TL;DR: Import as a Non-BlueJ project to run in BlueJ.
When dealing with Java projects containing subfolders, BlueJ creates unique package.bluej for every single subfolder. This can be a hassle with multi-folder projects. Importing as a non-BlueJ project is easier than having Git store a new BlueJ file for every empty folder.