Develop command‑line interface (CLI)

[aalexmmaldonado]

Description
Design a command‑line tool atomea using Click or Typer to expose key package functionality. Subcommands should enable users to digest data, run workflows, and export results without writing Python code. Provide clear help messages and sensible defaults.

Key tasks:

• Create CLI entry point in pyproject.toml and setup.cfg/setup.py.
• Implement subcommands: digest, run-md, run-dock, export.
• Support global flags for config files, verbosity levels, and output paths.
• Generate shell completion scripts and man pages.

Acceptance Criteria

• Users can invoke atomea digest --help and see detailed usage instructions.
• Integration tests call each subcommand in a temporary directory and validate output files.
• Shell completions generated for Bash, Zsh, and Fish.
• Documentation includes a CLI reference section.