I spent the last couple of days frustrated with the flex rig file. I asked a question on blender exchange, but no one answered: https://blender.stackexchange.com/questions/167308/cg-cookie-flex-rig-linking-problems

There were 4 problems

1. Invalid drivers and cyclic dependencies
   • I was thinking these were the reason for the other issues I list below. Turn out not, but I cleaned them up. I had to write some python scripts to cipher through all the drivers and find the invalid ones. At one point I had to open the blend file in a hex editor and look for a driver that was bad but I couldn't see it through the interface.
2. The rig wasn't visible after I make proxy. It was hidden behind the linked character.
   • I describe how I solved this problem in this video
3. The bone shapes had modifiers on them, which disappear when I execute the rig_ui script (or under other mysterious circumstances)
   • I just had to apply the modifiers so they don't disappear
4. The IK leg was bending backwards. So the knee would bend backwards instead of forwards. Reminded me of the aliens in that Charlie Sheen movie (Arrival)
   • I describe how I solved this issue in the same video above.

Have to admit this behaviour is kinda weird all around. Not sure if it's because the file was originally 2.79 or what. When I use rigify with MB-Lab things were a lot smoother. Anyway, moving on.

FYI, the file can be downloaded from here