Fixes 5.0.0rc

Fixes to some apps to run with 5.0.0rc-beta.

Some other examples still seem to be broken and need to be fixed by @mandli

```

=============================================
/Users/rjl/Downloads/clawpack-rc-beta/apps/multilayer/2d/plane_wave
=============================================
Makefile:214: /src/Makefile.common: No such file or directory
make: *** No rule to make target `/src/Makefile.common'.  Stop.

=============================================
/Users/rjl/Downloads/clawpack-rc-beta/apps/storm_surge/atlantic/irene
=============================================
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/holland_storm_module.f90:74.66:

        real(kind=8) :: forecast_time,last_time,x(2),y(2),ds,dt,dx,dy,theta
                                                                  1
Warning: Unused variable 'dx' declared at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/holland_storm_module.f90:74.69:

        real(kind=8) :: forecast_time,last_time,x(2),y(2),ds,dt,dx,dy,theta
                                                                     1
Warning: Unused variable 'dy' declared at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/holland_storm_module.f90:74.75:

        real(kind=8) :: forecast_time,last_time,x(2),y(2),ds,dt,dx,dy,theta
                                                                           1
Warning: Unused variable 'theta' declared at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/constant_storm_module.f90:139.37:

        real(kind=8) :: x, y, r, r_km, R_eye(2), f, C, w
                                     1
Warning: Unused variable 'r_km' declared at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/constant_storm_module.f90:110.31:

        real(kind=8) :: junk(2)
                               1
Warning: Unused variable 'junk' declared at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/constant_storm_module.f90:101.52:

    real(kind=8) function constant_storm_direction(t,storm) result(theta)
                                                    1
Warning: Unused dummy argument 't' at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/stommel_storm_module.f90:70.58:

                                        xlower, ylower, dx, dy, t,aux, &
                                                          1
Warning: Unused dummy argument 'dx' at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/stommel_storm_module.f90:70.65:

                                        xlower, ylower, dx, dy, t,aux, &
                                                                 1
Warning: Unused dummy argument 't' at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/stommel_storm_module.f90:70.46:

                                        xlower, ylower, dx, dy, t,aux, &
                                              1
Warning: Unused dummy argument 'xlower' at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/storm_module.f90:309.61:

    real(kind=8) pure function no_wind_drag(wind_speed, theta) result(wind_drag)
                                                             1
Warning: Unused dummy argument 'theta' at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/storm_module.f90:309.54:

    real(kind=8) pure function no_wind_drag(wind_speed, theta) result(wind_drag)
                                                      1
Warning: Unused dummy argument 'wind_speed' at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/storm_module.f90:294.65:

    real(kind=8) pure function garret_wind_drag(wind_speed, theta) result(wind_
                                                                 1
Warning: Unused dummy argument 'theta' at (1)
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/friction_module.f90:141.12:

            aux(friction_index,:,:) = manning_coefficient
            1
Error: Incompatible ranks 2 and 1 in assignment at (1)
make: *** [/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/friction_module.mod] Error 1

=============================================
/Users/rjl/Downloads/clawpack-rc-beta/apps/storm_surge/atlantic/sandy
=============================================
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/friction_module.f90:141.12:

            aux(friction_index,:,:) = manning_coefficient
            1
Error: Incompatible ranks 2 and 1 in assignment at (1)
make: *** [/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/friction_module.mod] Error 1

=============================================
/Users/rjl/Downloads/clawpack-rc-beta/apps/storm_surge/gulf/ike
=============================================
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/friction_module.f90:141.12:

            aux(friction_index,:,:) = manning_coefficient
            1
Error: Incompatible ranks 2 and 1 in assignment at (1)
make: *** [/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/friction_module.mod] Error 1

=============================================
/Users/rjl/Downloads/clawpack-rc-beta/apps/storm_surge/gulf/katrina
=============================================
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/friction_module.f90:141.12:

            aux(friction_index,:,:) = manning_coefficient
            1
Error: Incompatible ranks 2 and 1 in assignment at (1)
make: *** [/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/friction_module.mod] Error 1

=============================================
/Users/rjl/Downloads/clawpack-rc-beta/apps/storm_surge/square_basin
=============================================
/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/friction_module.f90:141.12:

            aux(friction_index,:,:) = manning_coefficient
            1
Error: Incompatible ranks 2 and 1 in assignment at (1)
make: *** [/Users/rjl/D/clawpack-rc-beta/geoclaw/src/2d/shallow/surge/friction_module.mod] Error 1


```