[runtime] remove stale cleanup artifacts

[GsCommand]

Motivation

• Remove unreferenced maintenance helpers that clutter the repo and increase upkeep cost.
• Clean up a duplicated comment block in server.mjs so the source reads clearly without changing behavior.
• Drop truly unused dependencies to keep package.json and the lockfile coherent and minimal.

Description

• Deleted orphaned helper scripts tools/patch-catch.mjs, tools/patch-sign-order.mjs, and tools/patch-smoke.mjs because they are not referenced by scripts, docs, CI, or runtime codepaths.
• Removed the duplicated /verify comment banner in server.mjs without altering any endpoint logic.
• Removed dotenv and node-fetch from dependencies in package.json and refreshed package-lock.json to reflect those removals.

Testing

• Ran npm run check which performs node --check server.mjs and the syntax check completed successfully.
• Ran npm test (unit tests + smoke) and all tests passed, including the unit TAP suite and the smoke checks.
• Verified the repo remains buildable and runtime behavior unchanged by exercising the code paths covered by the test suite.

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Codex Task