Devoncarew misc fixes2

@dinhviethoa @ussuri, various misc fixes:

- bind `command-,` to the setting dialog on the mac
- disable our favicon for now
- re-position the `Git Add` context menu item
- refresh entire projects when spark re-gains focus. This fixes an issue where we could refresh a parent and a descendent resource at the same time and end up adding new child resources to the resource tree several times