v0.6.3 — update stays in its lane

Fixed

• update installed graphyloop into tools you never added it to. It ran a
  full install, so every tool merely present on the machine got wired: MCP
  entry, agents, skills and commands. Without --harness it now refreshes only
  the tools graphyloop is already in. A stale or broken entry still counts, so
  repairs keep working. It lists the tools it leaves alone, and
  --harness <name> adds one on purpose. A machine with no graphyloop anywhere
  still gets a first install.