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Remove `[include_]system_hdf5_netcdf` #260

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Run time

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Job	Run time
lint with pre-commit	15s
test mache - python 3.9	1m 3s
test mache - python 3.10	1m 12s
test mache - python 3.11	1m 15s
test mache - python 3.12	1m 19s
	5m 4s