Complete end-to-end permission flow for tool execution:
- Add POST /api/permission/grant endpoint with gateway proxy
- Add permission checks for list_dir, edit_file, append_file tools
- Fix frontend PermissionPrompt to call grant API instead of chat messages
- Add grantPermission() to frontend API client
- Expose PermissionCache via AgentInstance for API access
- Wire up permission grant callback through gateway to agent loop
Inspired by opencode's permission system architecture.
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.
