GET of newick now takes bracket_ingroup flag

This used to be on by default. Now, there is an argument
bracket_ingroup=true
that allows the client to request comments that bracket
the ingroup definition in the newick.
This is not documented in the public APIs as a primary option.
It is mentioned on
  https://github.com/OpenTreeOfLife/phylesystem-api/tree/master/docs
Documentation of new flag.

This addresses:
    https://github.com/OpenTreeOfLife/opentree/issues/490
obscure bug fix: publication_DOI can be null

This cropped up when testing the previous commit - it probably
does not affect any real client code, because clients would
omit publication_DOI rather than sending in a null value.
A test script sent in a null value, without the check in this commit
that lead to an internal server error.
removing typo to enable option
Merge pull request #126 from OpenTreeOfLife/opentree-issue-490

Opentree issue 490 'Newicks from curator app not parsable'