Changes to agent.yaml tool connections are not updated during azd provision

[therealjohn]

also if I change any property of tools in manifest, azd provision does not take into account as azure.yaml is not updated.

[therealjohn]

To support this, and other configuration changes:

• pre-provision hook to take the current state of the agent manifest and do the same things that init does so that azure.yaml is correctly updated with any changes (name, tool connections, additional resources, etc.)
• if anything was added that requires new values, we need clear errors with azd env set <var> <value> so that devs can update it, and so agents can do it in --no-prompt mode.