chore: update pnpm version to 9 and remove "patches" directory from p… #623

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Run time

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Job	Run time
test (ubuntu-latest, 18)	1m 42s
test (ubuntu-latest, 20)	1m 36s
test (macOS-latest, 18)	1m 14s
test (macOS-latest, 20)	1m 22s
	5m 54s