IntelliJ doesn't recognize java project after cloning
You have to mark your src directory as Source Root.
Right-click on the src folder and select Sources Root:
Then you'll see that the icons will change:
EDIT
Check the output path by bringing up the Project Structure view.
Press Ctrl+Alt+Shift+S
Similar to what maba said above, but if applicable you probably want to mark main and test as source & test source directories (respectively). That's a common project directory structure where literally marking src (parent of main and test) as source won't work for you.