I'm using Arduino projects all the time and I have tried one to simulate, compile and upload in the simulator. The same project, the same source and corrections from the simulator itself. However, project and source code are separated currently.
Also, sometimes can be used two or more Arduino UNOs (for instance) in the same project, thus multiple sources should be allowed and also upload firmware to the right UNO. A bit of complication, I'm aware, but worth considering at least.