So this is a combination problem and solution. I scoured the forums, google, etc, looking for the fix, and ended up finding the fix on my own.
Anyway, the original symptom looked like a common
#include <bits/c++config.h> include path file not found issue. Like in this thread: https://github.com/esp8266/Arduino/issues/1631
The include path pointed to some of my MATLAB stuff and the related support packages.
I spent some time uninstalling an un-needed version of matlab 2016a, and continued to see the compile error. (failed compile, never getting to upload).
The final step was digging for where include paths and preferences were stored in preferences.txt.
After commenting them out, and restarting the IDE, the compile and upload worked successfully with the Blink example.