xmlui: Switch all XMLUI themes to non-caching Cocoon pipelines

We seem to be having overly-excessive caching on XMLUI and it's
causing our themes to show up incorrectly.  I'm not sure of the
performance implications of this for the server, but it seemed
to work well for the CCAFS theme initially and the issues are
persisting with other themes now so we might as well try.

Possibly related: https://jira.duraspace.org/browse/DS-298
Enable public usage statistics
input-forms.xml: Add new CCAFS communities to input-forms
messages.xml: Clean up title and trail for custom browse types
dspace.cfg: Set mandatory bitstreams to false

This accidentally became true when I merged the dspace.cfg into git
a few weeks ago.
Add ability to browse by Output Type

Requires an index-init to create the new browse / search indexes.
input-forms.xml: Add animal species to ILRI Journal submission template