Documentation [UMBRELLA]

Umbrella issue documenting work that needs to be done on the documentation

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GENERAL: General issues related to the documentation (e.g. structure)
- #191
- #473

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INFRASTRUCTURE: Issues related to installing MUSE and developer infrastructure (e.g. tests)
- #261
- #257
- #165
- #126
- #154

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TUTORIALS: Issues related to notebooks and tutorials
- #99
- #258
- #264
- #207
- #190
- #340
- #282
- #291
- #295
- #337

Notes:
- The main issue here is that the tutorials do not appear to be up to date with the current version of the code. A priority would be to bring the tutorials up to date, and ideally have a system in place which checks when tutorials need to be updated (#99)
- As a new user to MUSE, working through the tutorials was a confusing experience as my outputs almost never matched the figures in the documentation (or otherwise failed to run without error). Bringing the tutorials up to date would certainly help, but I also think more information needs to be added to fully describe the model configurations/parameters used to generate the figures (for example the `MaxCapacityGrowth` parameter appears to have been changed in 8.1, but this isn't documented). The aim is to give users all the information they need to replicate the figures, starting from the default model.
- For each tutorial, I think it would be very useful to have a very short summary to describe which files need to be changed when the user wants to add an agent/region/commodity etc.. This could be a 'checklist' of sorts. I think would be a very useful reference to guide users when the come to do this on their own, to ensure they don't accidentally skip any steps.
- I think some of the figures could be improved/clarified. e.g. for the line plots, what do the shaded regions indicate? There are a series of additional analysis notebooks together with the model files which create clearer figures, but these are unused in the documentation

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MODEL DESCRIPTION: Specific cases where the model description or background info needs improvement

Implementation details:
- #218
- #196
- #195
- #188

Inputs/parameters:
- #492
- #474
- #265
- #263
- #208
- #206
- #205
- #203
- #202
- #201
- #200
- #199
- #198
- #197

Outputs:
- #192