Update documentation with the cleaned history

[ekatef]

That is an improved version of #602 built on a cleaned fork of main (@davide-f thanks a lot for providing proper spells for it!)

This update is intended to improve clarity and usability of our documentation and is mainly based on inputs from @yerbol-akhmetov and @davide-f. (Yerbol and Davide, thanks a lot for an insightful discussion!)

The suggested fixes contain:

• revision on natura.tiff usage to account for the recent developments;
• clarifications on cutout usage;
• improvement of explanations on data clean-up.

Checklist

• I tested my contribution locally and it seems to work fine.
• Code and workflow changes are sufficiently documented.
• Newly introduced dependencies are added to envs/environment.yaml and envs/environment.docs.yaml.
• Changes in configuration options are added in all of config.default.yaml and config.tutorial.yaml.
• Add a test config or line additions to test/ (note tests are changing the config.tutorial.yaml)
• Changes in configuration options are also documented in doc/configtables/*.csv and line references are adjusted in doc/configuration.rst and doc/tutorial.rst.
• A note for the release notes doc/release_notes.rst is amended in the format of previous release notes, including reference to the requested PR.

[davide-f]

Good to me :) I'd merge if you have finished here

[ekatef]

Thanks @davide-f!

If you don't mind I'd be happy to add a couple points about time settings as discussed in #609 which seem to be well aligned the current content. However, if you feel like it'd be better to create another PR for that, I'm absolutely fine with it :)

[davide-f]

Ok! Then I'll wait ;)

[davide-f]

@ekatef given #612, can this PR be merged or shall we wait?

[ekatef]

@davide-f not yet :) In #612 @asv365 is addressing fine structure of doc/configuration.rst (previously some sections were captured from the wrong fragments).

Here we need a couple of additions to clarify which snapshot values are appropriate when customising the model. Sorry for the delay, will try to add these explanations today

[ekatef]

@davide-f added the promised points. If you approve these additions, I think this PR can be merged

[pz-max]

Let's talk at today's weekly about this PR. Looks good to me @ekatef