When you compile all the source files, you say @make all, and when compiling only the files you changed, you should just say @make. (When @make all stopped due to a compilation error, @make will be enough next time, because @make all `touches' all the files at the beginning.)
Before doing this, you have to do one thing: to specify the compiler option because it is quite system dependent. There is a csh envioronment variable foption in the file @make. It is passed to Makefiles in each directory. You need to change it for your system. Because of this, you cannot simply make in each directory without calling @make. Hopefully, an empty compiler option will do. (In the laset version CAIN, directories for include files were specified by a compiler option -I. Since this turned out to be system-dependent, the include statements in all the FORTRAN files in the present version, contains the directory names by relative paths.)