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Fixes for the parameter scaling changes in the trunk.

The scaling flag is no longer part of the specific analysis API optimisation methods. Instead the
pre-assembled scaling matrices are passed into all three API optimisation methods.

bugman 2014-07-24

changed /branches/frame_order_cleanup/specific_analyses/frame_order/api.py
changed /branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
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