Refactor + Include missing .it content

[fivegrant]

This fixes #80 and also refactors the decapodes directory to be more usable and readable. I tested Contexts and Configurations with Pydantic and they worked fine.

Trying to get this merged as soon as possible because it's needed for the simulation services and HMI integration

Issues

• The model InterType seems to be out of sync with the example Decapode. That's out of my wheelhouse so I'll defer to you @jpfairbanks and @olynch .
  • This may be an issue with main as well. I have not tested the model
  • The above issue also breaks SimulationPlan
• JSON Schema validates for any JSON: I think this is going to be an issue as people try to integrate against the spec.

[fivegrant]

I just tested main and the above issues I outlined above are not unique to this PR. I think we should go ahead and merge this, but if if you'd like to include fixes for the model intertype I'm fine with that as well

[jpfairbanks]

Just some small things like using joinpath and fixing indentation.