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fix to ensure HDF5 read/writes are row-major (Eigen default is col-major)

Jonathan Fisher requested to merge HDF5-fix into master

While working with Biodiff data that the HDF5 reader is not consistent w.r.t. row-major or col-major order for matrices. Eigen default is col-major, but the HDF5 specification requires row-major. This inconsistency should have been fixed in this commit (at least it is working properly with Biodiff data).

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