create an API for updating runtime parameters

For most runtime parameters, we read them at initialization and they never change. But we have a few cases where depending on the values of other parameters, we change some. This should be done explicitly through a setter function so we can catch changes when we transition to structs for the runtime parameters.

Here's a partial list of runtime parameters that we override:

• do_reflux (in Castro.cpp, read_params())
• rot_axis (in Castro.cpp, read_params())
• sdc_iters (in Castro_advance_ctu.cpp)
• small_temp, small_dens, small_pres, small_ener (all in Castro_setup.cpp)
• rotational_period (in Castro_io.cpp, scf_relax.cpp)
• point_mass (in Castro_io.cpp, Castro_pointmass.cpp)

Start by tracing the runtime-parameter initialization and override paths in Castro.cpp/read_params(), Castro_advance_ctu.cpp, Castro_setup.cpp, Castro_io.cpp, scf_relax.cpp, and Castro_pointmass.cpp. Define the setter API around the listed parameters and update those override sites so changes are explicit and ready for the transition to structs; verify every listed parameter uses the API.