chore: update jsonref, remove numpy dep, update ddtrace #3962

Job	Run time
Get Changes	5s
Check: source-shopify	45m 30s
Check: source-google-drive	4m 5s
Check: destination-motherduck	3m 8s
Check: source-intercom	2m 43s
Check: source-hardcoded-records	2m 28s
Check: source-pokeapi	1m 56s
	59m 55s

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