change some status_message to debug_message

These can be changed back if needed.  We still don't have an easy way to
show debug messages (or to log them).  These messages were switched due
to TCGA reference alignment builds spitting out hundreds of lines of
messages.
make reference_coverage semi-required

reference_coverage is only required if there are
reference_coverage_objects, e.g. a region_of_interest_set_name.
Merge branch 'anti-spam'

CHANGELOG: In an attempt to reduce the amount of information that gets
spammed to the screen when you start a reference alignment model we
have suppressed many messages that really only need to be displayed for
debugging purposes.  Next time you start a reference alignment model you
may feel like something is wrong because you are used to those messages
but we hope that this will provide a better experience.