fix: execute run-scoped Studio tools at runtime

[kojiwakayama]

Summary

• execute run-scoped injected Studio tools from the agent runtime before falling back to the shared registry
• keep registry-backed tools working unchanged when the config entry is true
• add runtime regression tests for inline configured tool resolution and execution

Testing

• deno test --no-check --allow-all src/agent/runtime/tool-helpers.test.ts src/server/handlers/request/agent-stream.handler.test.ts src/internal-agents/control-plane-auth.test.ts src/internal-agents/ag-ui-sse.test.ts src/internal-agents/session-manager.test.ts
• deno task verify:quick
• pre-push hook: formatting, lint, typecheck, deno task test:unit (1208 passed)