CLI Surface

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

The canonical runtime API root is apis/bijux-proteomics-runtime/v1; the compatibility mirror root is apis/agentic-proteins/v1.

Package Surface

• src/agentic_proteins/interfaces/cli.py is a compatibility CLI surface, not the preferred long-term operator surface
• new CLI affordances belong in the canonical runtime unless needed to preserve an existing contract
• CLI output drift should be treated as migration-sensitive behavior

First Proof Check

• src/agentic_proteins/interfaces/cli.py
• src/agentic_proteins/api/app.py
• packages/agentic-proteins/tests