Repair application naming and registration contracts

[codeforester]

Parent: #50

Train position: 5 of 22
Phase: P0 — Trustworthy lifecycle

Problem

Single-command naming ignores App.name, module-level registration is not runnable, and late or duplicate registrations can be silently lost after command materialization.

Acceptance criteria

• App.name controls the single-command Click name, help, and program identity consistently.
• The module-level @base_cli.command() API produces a retrievable, runnable stable command, or is replaced by an equally usable documented contract with compatibility handling.
• Registration freezes after Click command materialization.
• Duplicate command/subcommand names and late mutations fail deterministically.
• Single-command and group tests cover name, help, version, duplicates, and registration timing.

Dependencies

• None