Clean up documentation build warnings

[canyon289]

Description of your problem

When building docs there is a cascade of warnings, from reference issues to unused files. It would be great to clean these up as the preexisting warnings make it challenging to add docs, as new warnings are lost in a sea of red.

Namely there are some general categories of what needs to be done

Fix formatting issues that are raising warnings

/home/canyon/repos/pymc/docs/source/api.rst:38: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/canyon/repos/pymc/docs/source/api.rst:41: WARNING: Bullet list ends without a blank line; unexpected unindent.

Clear autodoc import issues

WARNING: autodoc: failed to import method 'Chain.init' from module 'transforms'; the following exception was raised:
No module named 'transforms'
WARNING: autodoc: failed to import method 'Chain.backward' from module 'transforms'; the following exception was raised:
No module named 'transforms'
WARNING: autodoc: failed to import method 'Chain.forward' from module 'transforms'; the following exception was raised:
No module named 'transforms'

Determine what to do with unlinked documents
/home/canyon/repos/pymc/docs/source/api/math.rst: WARNING: document isn't included in any toctree
/home/canyon/repos/pymc/docs/source/api/shape_utils.rst: WARNING: document isn't included in any toctree

There may be others as well

Dependencies

jupyter-sphinx==0.3.2
pydata-sphinx-theme==0.7.2
sphinx-copybutton==0.4.0
sphinx-design==0.0.13
sphinx-notfound-page==0.8
sphinx-remove-toctrees==0.0.3
sphinx-togglebutton==0.2.3
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5

[OriolAbril]

Transforms one should be fixed by #5347. Math and shape_utils ones were already fixed by #5439.

All the others will need to be addressed specifically, there are still many more issues, some of which are actually related to #5282, there are objects in the docs that have been moved or removed in v4 (probably missing ones too but that raises no warning) and docs are still documenting removed things or documenting things in their v3 place. #5439 is the furthest I could go, this will need someone familiar with v4 to check everything is documented and on the right place,or alternatively someone with time to do a thorough code review and check for missmatches with docs