handbook: add documentation for layers

Collections and overlays are deprecated in favour of layers, a much cleaner and
non-intrusive way of extending Poky with custom recipes, classes and
configuration.

This patch updates the Extending Poky section of the handbook to show how to
use layers to tailor Poky while dropping  the existing section on using
collections.

Signed-off-by: Joshua Lock <josh@linux.intel.com>

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