Clean makefiles and include directives.

Makefile.am

configure.ac

contrib/Makefile.am

examples/Makefile.am

examples/OASIS3_MCT_example.c

examples/OASIS3_MCT_example.sh.in

examples/dummy_atmosphere.F90

examples/dummy_atmosphere_c.c

examples/dummy_io.F90

examples/dummy_ocean.F90

examples/dummy_ocean_c.c

examples/perf_toy_cube.c

examples/perf_toy_icon.c

examples/toy_coupling.sh.in

examples/toy_icon_atm.c

examples/toy_icon_ocn.c

examples/toy_icon_runoff_atm.c

examples/toy_icon_runoff_ocn.c

examples/toy_mpiom_ocn.c

examples/toy_multi.sh.in