update: fix logic for updating layer dependencies at the end

* We were passing the incorrect path (to the top of the layer repo) if
  the layer had a subdirectory, so this doesn't seem to have been able
  to work for such layers previously.
* Doing this update in the main update.py script meant that this could
  never work across branches requiring a python version change (using
  PythonEnvironment records) since the code was running within the same
  environment in which update.py was launched - the entire point of the
  separation of the two scripts. Move the checking to update_layer.py
  and call it separately to perform these updates, splitting out some
  common code in order to do so.

Signed-off-by: Paul Eggleton <paul.eggleton@linux.intel.com>

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