documentation: clean up the input file documentation, add filterReactions parameter
documentation: clean up the input file documentation, add filterReactions parameter

Makes our recommendations known and gives basic
users less settings to look at

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