rename Makefile.am to Makefile.mk

Link: https://github.com/GeneAssembly/biosal/issues/628
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
fix compilation warnings with gcc (GCC) 4.8.2 20131212 (Red Hat 4.8.2-7)

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>