rename action_helpers.h to actions.h

Link: https://github.com/GeneAssembly/biosal/issues/677
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
use bitmap flags in workers (dead, debug, busy)

Link: https://github.com/GeneAssembly/biosal/issues/671
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
assembly: add messages for setting vertex flags

Link: https://github.com/GeneAssembly/biosal/issues/664
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>