For any other newbies like me who don’t already know how to add an Include path in Atmel Studio 7:
When you created the AS7 project from the Arduino sketch, it creates a Solution with two Projects, one named “ArduinoCore” and one with the name you chose for your Arduino sketch. In order to get AS7 to build correctly with SAMD-based projects (Zero, MKR1000, MKRZero, M0, Tian, etc.) you need to add the path to the Atmel CMSIS library in four places: one for the C compiler and one for the C++ compiler in the ArduinoCore project plus one for the C compiler and one for the C++ compiler in the project associated with your Arduino sketch.
To do this, in the Solution Explorer pane, right click the ArduinoCore project and select Properties. This will open the Properties pane. On the left, select Toolchain. Then under ARM/GNU C Compiler select Directories. Click the Add Item button and then enter the full path to the SAMD CMSIS files. Uncheck the Relative Path box and click on OK. Repeat this for the ARM/GNU C++ Compiler. Then repeat the process again starting with right clicking on the project associated with your Arduino sketch.
The path will look something like this:
These files are installed by the Arduino IDE when you use the board manager to install support for SAMD boards. Note that the path name may change with new releases of the Arduino IDE or board support packages, so verify the location on your system.