Makefile.amのサンプル
/project/Makefile.am
SUBDIRS = src src2

/project/src/Makefile.am
bin_PROGRAMS= hello
hello_SOURCES = hello.c

/project/src/hello.c
#include 
int main(void){
  printf("hello!!");
  return 0;
}

/project/src2/Makefile.am
bin_PROGRAMS=world
world_SOURCES = world.c

/project/src2/world.c
#include 
int main(void){
  printf("world!!");
  return 0;
}