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Add MANIFEST.in for packaging (#900) #1622

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Run time

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Job	Run time
target (ci_unit_tests)	17m 24s
target (integration_tests)	6m 19s
focal_self_test	57s
target (ci_housekeeping)	4m 41s
target (viral_assemble)	11m 27s
target (viral_refbased)	10m 15s
	51m 3s