Fix docs build warnings and generate API docs with `autosummary` extension

[yousefmoazzam]

Fixes #468 Fixes #486 Fixes #487 Fixes #490 Doesn't solve #492, but instead finds a workaround via not using | in conjunction with certain types

Checklist

• [x] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes
• [x] I have made corresponding changes to the documentation

[yousefmoazzam]

All warning in the docs build locally are gone, but the CI has one warning:

/home/runner/work/httomo/httomo/docs/source/developers/api.rst:4: WARNING: autosummary: failed to import httomo.cli.
Possible hints:
* AttributeError: module 'httomo' has no attribute 'cli'
* ImportError: cannot import name '__version__' from 'httomo' (/home/runner/work/httomo/httomo/httomo/__init__.py)
* ImportError: 

Since it appears in CI only and not locally, it may need a bit more time to debug, so I'll make an issue for it to tackle after this PR; it's small in comparison to the main aim of this PR which was to:

• get rid of as many easily tackle-able warnings in the docs build as possible (ie, get all the low hanging fruit)
• generate API docs and include them in the main index.rst