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BUG: Deep transform should affect the initial positions as well

Sreekanth Arikatla requested to merge sreekanth-arikatla/iMSTK:fixDeepTransforms into master

Deep transforms currently do not modify the m_initialVertexPositions. This poses a problem for a scene object on which deformation physics is run. This MR modifies the applyTranslation, applyRotation and applyScaling functions to also modify the initial vertex positions stored during the creation of the mesh/point set

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