Doing a "diff" on two seperate .qpf files

A couple of us students in class generated a design in Qsys that includes a NIOS II and several other modules that are irrelevant in mentioning here. We also wrote a c application in eclipse and downloaded the .elf file to the board. I had no issue in doing this but two friends of mine must of messed up somewhere along the line and were having problems downloading their .elf file to the board. I thought it might be informative to do a "diff" between certain files in my project folder to their files in their project folder since we both followed the same instructions through the entire design process. What files can I essentially do a diff on to spot obvious mistakes or issues that might cause an issue with downloading a elf file to our NIOS II design we made in Qsys?

It's important to note that many files were already given to us by the professor. The only tasks we had to do was the following....

Design a layout in Qsys with a NIOS II and several other modules
Generate the HDL files and run a compile in Quartus
Download the file to the DE10Lite board
Open up Eclipse and bring in our sopc file
Write a c application which was just a simple hello world program
Compile and download the elf file to the NIOS II design we designed/downloaded earlier in Qsys and Quartus

I believe my friends were able to get as far as the last step but couldn't proceed any further. I can't recall the error message they were having so I apologize for the lack of info. However, my question is more on what files would be the most ideal in doing a diff on. Thanks ~S