fix directory structure

bumploc/
   conus12km-401km11levels/
   hrrrv5-401km11levles/

graphinfo/
   conus12km_mpas.graph.info.part.*
   hrrrv5_mpas.graph.info.part.*

meshes/
   conus12km.*.nc
   hrrrv5.*.nc

mpassit/
   conus12km
   hrrrv5

physics/
and
stream_list/
   convection_permitting/
   mesoscale_reference/

jedi/

upp/

ungrib/

Vtables/
   Vtable.*