enable: save --telemetry and --absolute-git-hook-path on a configured repo

On a repository that was already set up, entire enable --telemetry=false (or --absolute-git-hook-path) without --agent routed to agent management, which writes strategy and checkpoint-backend flags but not these two, so it exited 0 having saved nothing. Write them with updateGlobalSettings, after the identity preflight, to the same target file the rest of enable uses.