refactor: Made `command` functions to access PackageManager unavailable from public API #3534

Job	Run time
run-determination	2s
check-outdated (./)	22s
check-config (./)	20s
check-formatting (./)	17s
check-style (./)	2m 8s
check-license-headers (./)	23s
build (arduino/discovery/discovery_client)	33s
build (client_example)	46s
build (commands/daemon/term_example)	50s
	5m 41s

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