## Why
MCP config refreshes previously retained session app overrides, leaving connector approval changes unapplied in existing sessions.
## What changed
- Refresh explicit session `apps` overrides alongside `plugins`, allowing updated link approval settings to take effect on the next turn.
- Preserve overrides for omitted sections and restore inheritance when a section is an empty table.
- Validate app overrides and the effective app configuration, rejecting refreshes that expose invalid inherited settings.
## Testing
Add coverage for independent and combined app/plugin updates, clearing overrides, and rejecting invalid inherited app settings. Add an integration test verifying that changing a link's approval mode from `approve` to `prompt` requests approval before executing the next turn's tool call.
GitOrigin-RevId: 3fa36744a9ccd9e735e4cda7f061ccff1cf2a269