Help with the Arduino to AtmelStudio conversion

So i used this walk through to utilize the debug capabilities of the Atmel Studio for my arduino project.

http://www.engblaze.com/tutorial-using-atmel-studio-6-with-arduino-projects/

Followed most of the steps (think its a little older version than AtmelStudio 6.2) with no problem. When i go to compile I get a ton of errors based on library files. I wonder if there was a setting i forgot to change when adding all the arduino libraries over that confuses the Atmel software.

I attached the picture of the library errors. Thoughts?