Although the present software is protected by the GNU General Public License, and the user should always get the source code, it is sometimes more practical to get a nicely described user interface to plug in your own routines, instead of having to analyze the whole program. Therefore, for specific tasks well-defined interfaces are put at the disposal of the user. These interfaces are basically FORTRAN subroutines containing a subroutine header, a description of the input and output variables and declaration statements for these variables. The body of the routine has to be written by the user.
To use a user subroutine, replace the dummy routine in the CalculiX distribution by yours (e.g. dflux.f from the distribution by the dflux.f you wrote yourself) and recompile.