We have added context sensitive help to many of the views in Protégé. If help is available for a view then that help can be shown by pressing the "question mark" button in the view header. Help documentation ultimately points to here.
We have also added help documentation for the class expression syntax that is used in Protege. The help documentation can be displayed via the help button on the class expression editor dialog. Documentation can be found here.
Fixed a problem where "Save" and "Save As" could produce different orderings for ontologies saved in Turtle syntax, which could cause problems with using version control systems to store ontologies.
Fixed a problem where the object property hierarchy would not be updated if the active ontology was changed (protegeproject/protege#606).