fix directory structure

bumploc/
   conus12km-401km11levels/
   conus3km-401km11levles/
   atl12km-401km11levles/

graphinfo/
   conus12km.graph.info.part.*
   conus3km.graph.info.part.*
   atl12km.graph.info.part.*

meshes/
   conus12km.*.nc
   conus3km.*.nc
   atl12km.*.nc

mpassit/
   conus12km
   conus3km
   atl12km

physics/
and
stream_list/
   convection_permitting/
   mesoscale_reference/

jedi/

upp/

ungrib/

Vtables/
   Vtable.*