chore: remove flaky e2e resource refresh test

The test relies on a hard waitForTimeout and an external package
(@modelcontextprotocol/server-everything) that other e2e tests avoid.
Dropping it to keep the PR focused on the bug fix.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: olaservo