PropertyHDF5: cleanup imports
Entities: dependency to front-facing classes part1

This is just the first of two steps
Entities: dependency to front-facing classes part2

Remove dependency from File in EntityHDF5. This step
requires changed in almost all classes of the hdf5
back-end.
Entities: dependency to front-facing classes part3

Remove dependency from Block in EntityWithSourcesHDF5. This step
requires changes many classes of the hdf5 back-end.
General: code cleanup and todo comments