Update (most of) indirect engine API docs
Update (most of) indirect engine API docs

dwhswenson/openpathsampling,choderalab/openpathsampling,choderalab/openpathsampling,openpathsampling/openpathsampling,dwhswenson/openpathsampling,openpathsampling/openpathsampling,choderalab/openpathsampling,dwhswenson/openpathsampling,openpathsampling/openpathsampling,openpathsampling/openpathsampling,dwhswenson/openpathsampling