Hi Sara:
Just to add to Alfred's nice response, a couple of points:
1) When we run WRF-Hydro offline (uncoupled to WRF), the version of the HRLDAS driver that we use for Noah-MP requires the wrfinput file to define some static fields for Noah-MP (e.g., land cover type, soil type) in addition to (on cold start only) LSM starting states for soil moisture, snow, etc. When you run with a restart file, the model will NOT use the initial soil moisture, etc. from wrfinput, but will still use that file to grab the static information (land cover type, etc.).
2) There is a bit of legacy duplication in that the hydro routing modules rely on the geo_em file for some of this static information, but Noah-MP shifted to pulling everything (static and initial condition fields) from wrfinput. As some point we will migrate the hydro codes to use wrfinput so only one file will be needed for both, but until then we still require both the geo_em and wrinput files.
Hope that helps...
Thanks!
Aubrey