Rerun and update Fundamentals notebooks

[hjstroud]

This needs to be done once Issue #111 is resolved, so that we can push a final version of these notebooks with up to date outputs for each cell to main.

• [x] Resolve #111

[hjstroud]

I think a lot of the information in these notebooks is still relevant for someone looking to understand more fundamentally how NanoVer works. It would be good to go through them and update information where necessary to link to the current structures used in NanoVer (e.g. the OmniRunner), but I don't think much of the code should actually be changed to use the new structures as it nicely illustrates the key concepts with some more fundamental classes on which the new objects are built.

The visualisations notebook needs a closer examination in itself (which has its own issue, see #192), so I will not include this notebook in the tasks to complete to close this issue.

Notebooks to update:

• [ ] commands_and_state.ipynb
• [ ] frame.ipynb
• [ ] servers.ipynb