robertbuecker/diffractem: Bugfixing, streamlining, refinement

Several new functions are included, especially regarding geometry/cell refinement and CrystFEL integration. Tested with the notebooks included in the submitted version of the workflow paper (available at https://github.org/robertbuecker/serialed-examples).

Probably the last release that keeps the peaks and predictions tables in the Dataset object and supports table-style HDF5 entries.