don't try to determine primary sample idx when not merging samples

Entry merging requires figuring out which entry should override another
in the case of collisions. This only happens when merging samples,
however. The test to see which entry is better only makes sense when
you have the same sample in multiple input files, and it is expensive.
Now we don't do it when we're just doing a simple merge with no sample
collisions.
help and version messages now go to stdout and return 0

They were handled by the general exception handler which printed to
stderr and returned 1.

closes #4