On Definition Rule Issues

The last time I worked on Nybble (about a year ago?) I started to set up Nybble to start running code, however, I only finished part of the setup. Since then it looks like the process has changed, and while I think I effectively finished the new setup process, I keep running into issues when I try uploading a sketch. I tried uploading the most recent files off of GitHub, but I keep getting a long string of errors including "___ was previously declared", "implicit pointer mismatch", and "code may be misoptimized unless -fno-strict-aliasing is used". Not really sure what to do, especially about functions being previously declared because the error message only shows them being declared in one place. While it is redundant, I have attached the full stack trace.