docs/tools: Improve output and checking for gen-doc.sh

Used to generate ontology reference documentation
docs/tools: make gen-doc.sh more portable, don't use /bin/bash

https://bugzilla.gnome.org/show_bug.cgi?id=722353
docs/reference: Use gtkdocize --flavour no-tmpl to avoid -chmod issue

Suggested in actual gtkdoc bugfix here:
https://bugzilla.gnome.org/show_bug.cgi?id=701259
docs/reference/ontology: Make output cleaner when generating ontology docs