Once you completed all tasks inside a project you can mark it done by clicking on mark done icon while hovering over the project with your mouse.
If you don't see this menu, you may have to click the "..." icon at the right:
If you don't see that, then make sure the "Hover button actions" strategy is enabled. If you have this strategy on and see the menu, but you don't see the "Mark done" button, then you may have removed it in the "Hover button actions" strategy settings. Just edit the strategy settings again to add this action.
Right click
You can also right click a project to mark it done.
You may have to enable or configure the Right-click menu strategy if this doesn't work for you.
Marking a project done in the project overlay
In the project overlay a "mark project done" button will appear at the top right once all tasks are checked off.
Troubleshooting - I can't mark a project done
If a project still has open tasks you will see the button but it can't be clicked. If you don't see any open tasks, switch to the backburner to see if there are any backburner tasks still in that project.