Add a processing command

1. Identify the input/output types and task sequence. Reuse a recipe in python/batchalign/recipes.py or add one that constructs Pipeline.
2. Implement a command module under python/batchalign/cli/. Use resolve_inputs for multiple paths and file lists, and cli_options(ctx) for global settings.
3. Pass opts.parallel as the recipe’s workers value. Use Interface for progress and the shared output helpers for outcomes where their contract fits.
4. Register the module in _LAZY_SUBCOMMANDS in cli/__init__.py. A file under cli/hidden/ is not automatically a public command.
5. Test help, argument validation, output destinations, and failures. Exercise a real invocation through just batchalign cli.
6. Add a task-focused how-to page and update the CLI reference.

morphotag.py demonstrates staged CHAT preprocessing; convert.py demonstrates output collision checks. Use the example that matches the new command’s behavior. See Pipeline architecture for the runtime.