Dialog: Deprecates some methods and fix the build with --warnings=fatal

* dialog.[hg|ccg]: Deprcate set_alternative_button_order_from_array(),
  alternative_button_order() (which have no deprecation advice in
  GTK+, but I have given up filing bugs about that) and
  get_action_area() (which does).
Main: Undeprecate add_gtk_option_group(), because it is still needed.

* gtk/src/main.[hg|ccg]: We should probably move it out of Main,
  along with some other functions from here, but Main does not feel
  completely deprecated anyway because Application still cannot
  properly handle GOption.
Wrap GtkActionBar

Bug #723124
Wrap new symbols added to GtkHeaderBar as of 3.12

* gtk/src/headerbar.[hg|ccg]:
  Added decoration-layout object property,
  decoration-layout-set object property,
  has-subtitle object property,
  get_decoration_layout(), get_has_subtitle(),
  set_decoration_layout(), set_has_subtitle().
Wrap GtkPopover
Added a comment
Regenerated methods .defs
Regenerate enums .defs
Regenerate extra defs
Regenerate .docs .xml
Popover: Simplify some _CONVERSION() lines.

The reinterpret casts were unnecessary.
Wrap new GtkStack symbols as for 3.12

* gtk_stack_get_transition_running function
* gtk_stack_get_child_by_name function
* GtkStack::transition-running object property
Wrap GtkSettings new properties as of 3.12

* GtkSettings::gtk-decoration-layout property
* GtkSettings::gtk-shell-shows-desktop property
* GtkSettings::gtk-dialogs-use-header property
Gtk::Entry: Add set/get_attributes()

* gtk/src/entry.hg: Add set_attributes(), get_attributes() and the
"attributes" property.
Gtk::Builder: Add expose_[object|widget](), [set|get]_application()

* gtk/src/builder.hg: Add expose_object(), expose_widget(),
set_application(), get_application(). Remove some TODO comments.
* gtk/src/builder.ccg: Remove a TODO comment.
Update Doxyfile.in

* docs/reference/Doxyfile.in: Update for doxygen 1.8.4.
Make it more similar to glibmm's Doxyfile.in.
Wrap GtkFlowBox
Wrap new symbols in GtkPlacesSidebar

	* GtkPlacesSidebar::local-only object property
	* GtkPlacesSidebar::local-only getter/setter object methods
3.11.5
Gtk::Popover::pointing-to changed type

	* GtkPopover::pointing-to changed its type from
	* cairo_rectangle_int_to to GdkRectangle.