Remove commented out code and redundant conditional next.

If we decide this should complain about existing commands, we can bring
back the confess in uncommented form.
Remove commented-out condition.
I dare to remove parentheses (and quotation marks).
Remove commented-out obsolete property "file_id".

This used to hold the ID of the file storage in LIMS... but it hasn't
for a long time and they are discontinuing that storage, anyway.
Remove commented out alternate logic.
Remove commented-out reference to ancient Picard version.
Remove useless sorting.

Even if it was once useful, the algorithm was mostly commented out and
we now use UUIDs that don't sort in a meaningful order.
Remove old comments, and add an example that uses the name.
Remove commented-out code from before the redaction.
Remove commented-out code from before the redaction.
Remove old commented-out code.

We must not want to ask, since we haven't come back to enable this!
Update the expected test-case.
Merge pull request #340 from tmooney/remove_commented_code

Clean Up Old Comments and Commented-Out Code