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Fixed reintegration post-refinement

Raza, Zamaan requested to merge refiner_reintegration into develop

Resolves #210 (closed)

The ShapeCollection attached to a PeakCollection is not saved in the experiment state hdf5 file, so if it is reloaded, any integration will silently fail. This merge request adds ShapeDialog to SubframeRefiner to rebuild the ShapeCollection before integration.

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