Clean up retired checklist command leftovers

[robertDouglass]

Summary

The checklist command was retired, but 3.2.0a9 still has leftover references that make the command surface look inconsistent. This is cleanup debt rather than an immediately observed runtime failure, but it can mislead release validation and future command/skill installation work.

Evidence from 3.2.0a9

• Installed CLI: spec-kitty-cli 3.2.0a9.
• src/specify_cli/skills/command_installer.py says checklist was retired in 3.2.0a5.
• src/specify_cli/shims/registry.py still includes checklist in CONSUMER_SKILLS and PROMPT_DRIVEN_COMMANDS.
• The packaged software-dev/command-templates/ directory does not include checklist.md.
• src/specify_cli/runtime/agent_commands.py still says the global installer writes all 16 consumer-facing commands, but the installed global command roots currently contain 15 spec-kitty.* command files.

Why this matters

The system appears to have two competing truths:

1. checklist is retired and should not be installed.
2. The registry/docs still classify it as a consumer-facing prompt-driven command.

That can cause future cleanup, verifier, migration, installer, or docs work to reintroduce the command or report misleading command counts. It also makes it harder to tell whether a fresh install is actually current.

Suggested fix

• Remove checklist from the active consumer command registry if it is truly retired.
• Update docstrings/user-facing counts from 16 to 15 where applicable.
• Keep any retirement/removal logic needed to delete stale pre-3.2.0a5 files.
• Add/adjust a regression test that asserts the installed command registry, packaged command templates, and generated command counts agree.

Acceptance criteria

• Fresh global command install no longer has registry/template/count disagreement around checklist.
• No stale spec-kitty.checklist* command is generated for supported agents.
• Tests cover the retired-command case so cleanup logic does not resurrect the command.