feat(agent-v2): resolve Dify core tools in agent runtime runner

[linw1995]

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Summary

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Checklist

• This change requires a documentation update, included: Dify Document
• I understand that this PR may be closed in case there was no previous discussion or issues. (This doesn't apply to typos!)
• I've added a test for each change that was introduced, and I tried as much as possible to make a single atomic change.
• I've updated the documentation accordingly.
• I ran make lint && make type-check (backend) and cd web && pnpm exec vp staged (frontend) to appease the lint gods