This PR addresses two issues reported by Sphinx. First, the
`docs/api/python/base/modes.rst` document was not included in any
toctree. Second, the `proofrule.rst` and `cvc5proofrule.rst` documents
were included in multiple toctrees. The latter is resolved by including
each document in only one toctree and referencing it elsewhere in the
documentation using cross-references.
