Add full API reference to the documentation

[ijpulidos]

    @xiki-tempula  Thanks for the feedback! This is definitely something that should be improved with the documentation. Even the classes have [docstrings with examples](https://github.com/choderalab/openmmtools/blob/2e64980d86cf087f69e282927eebf2b41b73a3ea/openmmtools/multistate/replicaexchange.py#L113-L206) that may help users figure out how to use them.

Maybe just by having a raw "API reference" in the documentation page will help with these cases.

Originally posted by @ijpulidos in https://github.com/choderalab/openmmtools/issues/631#issuecomment-1338449469