WIP: update docs for SII and other changes

[isaacsas]

A very large number of examples throughout the docs now error due to using Symbols in ways that are no longer supported / work so we are going to have to update all over to get things working again. We can work on it in this PR.

[ChrisRackauckas]

One thing to make sure is with the getp/setp and getu/setu we should show properly caching the function for a lean cost function.

[isaacsas]

If you look at the tutorial I updated I repeatedly reuse the function on different objects (problems, integrators, and solutions). But probably in the callback section we should emphasize that this should be precomputed and stored in the callback.

[isaacsas]

@TorkelE can you handle the remaining errors? They are from

1. SDE related indexing (just needs the SII/SciMLBase fixes, then we need to bump the doc/Project.toml to the right SciMLBase release).
2. Issues with the BifurcationTutorial
3. Broken links in a number of the tutorials.
4. Unreferenced footnotes in many tutorials. (I've made this only be warnings, but it would be good to fix them.)

You should be able to push directly to this PR, but let me know if you can't.

[isaacsas]

I also suggest doing a full local doc build once everything is fixed, and carefully looking through all the tutorials to check the outputs / figures are working and look correct (given that we can no longer preview it via CI).

[TorkelE]

Will have a look. I had a look through earlier and stuff should be fine, but maybe something appeared. Unreferenced footnote are intentional. They are basically further readings for some cases, but where I don't directly reference them in the tutorial.

[TorkelE]

I try to build local, but that fails on my computer these days (or most Julia code), which limits its utility.

[TorkelE]

There are a couple of indexing PRs up already that should fix some of the issues, so will go through once that is passed.

[isaacsas]

Sounds good! If it is failing on your computer have you deleted the manifest in the docs folder and re-resolve/updated using doc/Project.toml?

[TorkelE]

will try that, thanks :)

[isaacsas]

I assume this has been handled / will be handled in other docs so closing.