Add documentation on all the miscellaneous input options.
Add documentation on all the miscellaneous input options.

enochd/RMG-Py,comocheng/RMG-Py,pierrelb/RMG-Py,chatelak/RMG-Py,pierrelb/RMG-Py,chatelak/RMG-Py,nyee/RMG-Py,nickvandewiele/RMG-Py,enochd/RMG-Py,nyee/RMG-Py,nickvandewiele/RMG-Py,comocheng/RMG-Py