This has been bugging me for years and curiosity has finally gotten the best of me. If you create a project with File->New->Project From Existing Source the resulting project only shows any "src" folder. But doesn't show other directories. This is vastly different behavior that File->New->Project which results in a project that shows all sub-directories.
For example if you have a layout like this:
If you use Project from existing source the project view in intellij will only show the "src/" directory.
However, if you use New->Project and select the directory that has sources in it you get a project where project view shows all the directories.
Why? What is the point of Project from Existing Sources if it results in a project that doesn't show all the other directories?
Project created with File->New->Project... (then pointing at the existing directory):
Project create with File->New->Project from Existing Sources (this view is worthless):