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You will find two Makefiles in your project directory fhp.mk and fhpf.mk. Let's talk first about fhpf.mk.
In fhpf.mk you find a list of all FORTRAN and C source and include files for FASTEST3D except funcbcs.F, funcprp.F and funcusr.F which are project specific.
This Makefile will be included by the main Makefile (fhp.mk). If you want to add a file to be compiled or hold of an obsolete/not used file from compiling you should add/delete the filename in this (alphabetical) list.
So if you wrote a subroutine in the new file foo.F and you want this file to be compiled into FASTEST3D then you have to asure that foo.F is listed in fhpf.mk.