Docs: Remove extra indentation during Sphinx build
Many of our docstrings have excessive indentation, so the docstrings end up with quotation blocks when rendered by Sphinx. Ideally, this should be fixed in the docstrings, but we have over 700 docstrings...
An easy interim fix is to clean this up while Sphinx is processing the lines. We already do some reprocessing of the docstrings, so it is straight forward to add.
The unused code in doc/conf.py was removed.
A few of the actual docstrings were fixed, where necessary, to get things working better.

