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.
Add comprehensive documentation including:
- CLAUDE.md for build instructions and environment setup
- project-map.md for directory structure and key file overview
- docs/reference/tools-api.md for detailed tools API and architecture
- session-log.md for tracking development decisions
- updates to plugin tool injection documentation regarding security risks