Minor boutcore cleanup

[dschwoerer]

There are some additional references in the documentation to hdf5, I didn't check them ...

git grep -i hdf5 
CHANGELOG.md: (skipped)
bin/bout-v5-macro-upgrader.py:        "old": "HAS_HDF5",
bin/bout-v5-macro-upgrader.py:        "old": "HDF5",
change_summary.md:- Fix an issue with text attributes in HDF5 files
manual/sphinx/developer_docs/file_io.rst:developed at LLNL [1]_. HDF5 was also previously supported. To
manual/sphinx/user_docs/advanced_install.rst:   ./configure --with-netcdf=/usr/local/tools/hdf5-gnu-serial-1.8.1/lib --with-fftw=/usr/local --with-pdb=/usr/gapps/pact/new/lnx-2.5-ib/gnu
manual/sphinx/user_docs/advanced_install.rst:   ./configure --with-netcdf=/usr/local/tools/hdf5-gnu-serial-1.8.1/lib --with-fftw=/usr/local/tools/fftw3-3.2 --with-pdb=/usr/gapps/pact/new/lnx-2.5-ib/gnu
manual/sphinx/user_docs/advanced_install.rst:   module load hdf5/1.8.17--intel--pe-xe-2017--binary
manual/sphinx/user_docs/advanced_install.rst:Then download source code for hdf5-1.12.0 (hdf5 is available in a module on
manual/sphinx/user_docs/advanced_install.rst:* hdf5-1.12.0::
manual/sphinx/user_docs/advanced_install.rst:    ./configure --prefix /directory/to/install/hdf5 --enable-build-mode=production
Binary file tests/integrated/test-io/data/benchmark.out.0.nc matches
Binary file tests/integrated/test-io/test_io.grd.nc matches