add reference options dir and change default options template

gen_options.sh

reference/options/AGECLASSES

reference/options/AGECLASSES.oldformat

reference/options/COMMAND

reference/options/COMMAND.alternative

reference/options/COMMAND.namelist

reference/options/COMMAND.oldformat

reference/options/COMMAND.reference

reference/options/IGBP_int1.dat

reference/options/OUTGRID

reference/options/OUTGRID_NEST

reference/options/RECEPTORS

reference/options/RECEPTORS.namelist

reference/options/RECEPTORS.oldformat

reference/options/RELEASES

reference/options/RELEASES.alternative

reference/options/RELEASES.reference

reference/options/SPECIES/SPECIES.README

reference/options/SPECIES/SPECIES_002

reference/options/SPECIES/SPECIES_003