### Features
- Added `cwd` option to command reply config so external reply commands (e.g., Claude Code) run in the intended working directory for correct context.
- Added configurable file-based logging (default `/tmp/warelay/warelay.log`), with level set via `logging.level` in `~/.warelay/warelay.json`; `--verbose` still forces debug.
### Developer notes
- Command auto-replies now pass `{ timeoutMs, cwd }` into the command runner; custom runners/tests that stub `runCommandWithTimeout` should accept the options object as well as the legacy numeric timeout.