HDF5 Updates#5

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QuLogic wants to merge 4 commits intogeodynamics:masterfrom

Commits on Oct 1, 2015

Replace outdated INCLUDES with AM_CPPFLAGS.
Elliott Sales de Andrade
committed
Update HDF5 calls to work with 1.8+.
Elliott Sales de Andrade
committed
Update build to use new HDF5 macro.
Elliott Sales de Andrade
committed
Update manual about new HDF5 build macro.
Elliott Sales de Andrade
committed