refactor(permissions): add PermissionsContainer struct for internal mutability (#17134)

Turns out we were cloning permissions which after prompting were discarded,
so the state of permissions was never preserved. To handle that we need to store
all permissions behind "Arc<Mutex<>>" (because there are situations where we
need to send them to other thread).

Testing and benching code still uses "Permissions" in most places - it's undesirable
to share the same permission set between various test/bench files - otherwise
granting or revoking permissions in one file would influence behavior of other test
files.

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