That, and Everything needs to be converted over to C#. Though luckily the syntax of C++ is pretty similar to C#, but there are still a lot of differences. So the rewrite is not as bad as it could be but it is still pretty bad and quite boring / bad for motivation to redo something.
Sounds great! C# is more my ballgame, so I might even be tempted to contribute!
There is a user directory in Godot, which content can be added to. Simply have the game load the Simulation Parameters from there, and BAM. Instant moddability.
I’m back, and waiting for Godot’s implementation! 
Once it’s done in C#, I can make a proper attempt at joining the team, lol.
Why are you waiting for the release of 0.5.0 before getting started? The code is already on github: GitHub - Revolutionary-Games/Thrive: The main repository for the development of the evolution game Thrive. along with the setup instructions: Thrive/doc/setup_instructions.md at master · Revolutionary-Games/Thrive · GitHub
The full 0.5.0 release will likely just contain some more reimplemented features, compared to what is currently done.
Who is going to put all the json files there? The game would likely have to first write the json files to the user directory for them to be edited. And that would also need the json files to contain version information so that when we change the files the game will overwrite the old files. Also that way people wouldn’t be able to add any textures or models. So not instant moddability.
Well, in one of my godot projects I’ve been able to load audio files from the user directory, so it’s not impossible to load entirely new assets. You just need to have the game iterate over all assets in the directory, and copy them into the game directory (likely with a filter though).
Godot conversion completed at 84%.