Support updating Agents through API/SDK with the new YAML config setup

[elisalimli]

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🔖 Feature description

We should find differences between the old and new config and apply the changes.

Also, sync with the database. In case somebody doesn't change their config YAML, but delete a tool/datasource/assistant using our other API endpoints.

📝 Additional Context

No response

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[homanp]

@elisalimli the best thing to do here is to just delete the yaml and recreate it everytime a patch is made. You can make an utility method that handles this.