Agent tool auto-approval preferences reset

What changed

Legacy agent allowed_tools auto-approval preferences are not migrated to the new disabledTools model. Existing agents start with no manually disabled tools after migration.

Why this matters to the user

Tools that were previously auto-approved may ask for confirmation again under the new permission model. Manually disabled tools are now managed through the agent's disabled tools setting.

What the user should do

Review each agent's tool settings after upgrading and disable any tools that should be blocked.

Notes for release manager

This is a semantic model change: legacy allowed_tools represented auto-approval preferences, while disabledTools is a hard opt-out block.