Integrate `PermissionCache` into `WriteFileTool`, `EditFileTool`, `AppendFileTool`, and `ListDirTool` to allow user approval for actions outside the workspace.
- Add `PermissionPrompter` interface and `TerminalPrompter` implementation.
- Update `AgentInstance` to initialize and register the permission cache and `RequestPermissionTool`.
- Refactor filesystem tools to support permission checks via a `PermissionChecker` interface.
- Add `plan.md` documenting the multi-wave permission implementation strategy.
