Make sure dWdt always has the correct size

This eliminates issues reading the first profile written, where reading the
zero-size array can generate errors in h5py.
Remove a bit of dead code from BilinearInterpolator
Change logic to eliminate "signed/unsigned comparison" warnings
Fix to avoid overriding non-inflow boundary conditions
Fix logic error in determining whether to call setBoundaryValues

setBoundaryValues should be called only if the user has actually supplied a
value for one or more of the specified options, but the check being made
resulted in setBoundaryValues being called in almost all cases.