R1: move tool registry off Config onto Agent

The tool set is no longer part of the per-turn Config snapshot. Agent now
owns a ToolRegistry (created empty at init), populated via the new
Agent.registerTool / registerToolSource methods. openStream and
OpenStreamFn take the registry as an explicit parameter rather than reading
it from cfg.registry, so swapping provider/model between turns (setConfig)
no longer disturbs the tool set.

CLI migrated to register the Lua tool source onto the agent instead of a
locally-owned registry. Test harnesses updated to stage tools on the agent.

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