So, I’ve figured out the issue and it was a combination of bad logic and not being totally familiar with the automake/autotools world. I was adding the correct files to my Makefile.am template, but I wasn’t sure which step in our build process actually created the makefile itself. So, I was compiling with an old makefile that had no idea about my new files whatsoever.
Thanks for the responses and the link to the GCC FAQ. I will be sure to read that to avoid this problem occurring for a real reason.
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