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Added Miller index metadata to Peak3D

Raza, Zamaan requested to merge miller_indices into develop

Resolves #116 (closed).

Miller index data was previously not stored in any core object, instead being calculated as needed. In this branch I have added a MillerIndex object as a private member of Peak3D. It is assigned with a function call or for all peaks in a collection when Experiment::assignUnitCell is called. I have also removed some unnecessary function calls to compute Miller indices, reducing the computational overhead.

Note that this also includes changes from !114 (merged), so please look at that first.

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