Fix post-upgrade skill sync to refresh installed skills only

[hopelynd]

Summary

• After CLI auto-update and bl update, sync skills with bl skill update instead of bl skill init, so removed skills are not reinstalled (Allow opting out of auto-update and of the automatic bl skill init after updates #200)
• Keep bl skill init for first-time / full bootstrap; update agent docs and protocol versioning guidance to match
• Extend unit coverage for both binary and npm upgrade paths to assert skill update, not skill init