CLI Surface

CLI documentation should describe the commands the package truly owns, not the commands a reader might wish existed.

Package Surface

• src/bijux_proteomics/cli.py and interfaces/cli.py are the command-line surfaces for core contract workflows
• CLI behavior should reveal contract meaning and validation state rather than runtime orchestration detail
• new CLI promises must stay aligned with the stable contract model

First Proof Check

• src/bijux_proteomics/program_spec.py, programs.py, and targets.py
• src/bijux_proteomics/cli.py and interfaces/cli.py
• packages/bijux-proteomics-core/tests