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Remove `[include_]system_hdf5_netcdf` #258

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Run time

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Job	Run time
lint with pre-commit	14s
test mache - python 3.9	1m 1s
test mache - python 3.10	1m 9s
test mache - python 3.11	1m 13s
test mache - python 3.12	1m 15s
	4m 52s