Add intro in Docs + include a "MOM6 file structure primer" section

[ashjbarnes]

Add explanations about what each input and output file does. There are some general pointers mixed in that I thought of as I went. Intentionally informally written because documentation is often very boring

closes #145

[navidcy]

@ashjbarnes the file-structure.md is a bit too much, in the sense it reads like MOM6 documentation. We shouldn't need nor want to reproduce the MOM6 docs here. I'm shortening it.

[navidcy]

OK. Well it's fair, but I admit it wasn't clear to me! I'll rephrase and ask you to have a look in case I write something wrong!

[ashjbarnes]

OK fair!

But if (some of) the information is related to MOM6 then we should open a PR in the MOM6 docs and add the info, not "hide it" in a package about regional configurations.

Yeah that’s a tricky one. I’d intended for the section to be helpful for troubleshooting for the package but so much of the troubleshooting is linked to mom6. I’ve already made a PR into mom6 docs many months ago but due to the dev cycle those changes still haven’t been merged into main docs. If i push this then it might be 6 months until it appeared publicly, by which point we hope to have the paper well on its way

[navidcy]

OK. We can have this here but somehow the Docs section could be renamed. E.g. it can be a Tutorial of MOM6 or something...
I'll think about it. And we open a PR in MOM6 and when it's merged there we remove it from here.

[ashjbarnes]

OK. Well it's fair, but I admit it wasn't clear to me! I'll rephrase and ask you to have a look in case I write something wrong!

Yes good you picked this up! Need to explain more carefully. Perhaps need to explain that for rectangular domains the package holds your hand a lot, and for deviations from this people should use the base example and modify it to suit their boundaries. Later on we might have more examples for things like Panan which would be cool! But for now just the one

[ashjbarnes]

OK. We can have this here but somehow the Docs section could be renamed. E.g. it can be a Tutorial of MOM6 or something... I'll think about it. And we open a PR in MOM6 and when it's merged there we remove it from here.

Could do. My changes (explaining the data override which I linked in the text of this PR) were merged fairly quickly to the gfdl/dev branch but it seems to take a long time to make its way to the main branch

[navidcy]

I pushed a few changes!
lgtm now!

[navidcy]

@ashjbarnes can you have a look at my edits/suggestions?
a preview of the docs is at --> https://regional-mom6--148.org.readthedocs.build/en/148/

[navidcy]

If you agree with everything then merge! It's definitely a great start! We can modify later.

[navidcy]

Can we revert this last commit a16bfcd?

[navidcy]

I think it belong to a PR on its own

[navidcy]

OK, perhaps we can leave it. I realised that the segment class is not tested though.

[ashjbarnes]

OK, perhaps we can leave it. I realised that the segment class is not tested though.

Segment class is tested along with the expt class I think? Expt calls segment

[ashjbarnes]

Ok cool I'm happy to merge!

[navidcy]

how come the tests didn't break when we changes the segment class from args to kwargs?
I presume it's not used in the tests... but we can deal with that in a different PR