Consider approach to deprecated tools

[nathanjmcdougall]

Motivation
There are a few cases:

• The tool is deprecated because it no longer exists or is broken
• It exists but is no longer recommended (e.g. a better alternative exists)
• A special case of the above; it exists but a basically drop-in replacement exists (e.g. ruff)

How do we handle the above cases? An initial brainstorm:

For drop-in replacements, we can just change the config and migrate the user to the new approach automatically.

For non-recommended tools, we can spit a warning and recommend migrating.

For non-existent or broken tools, we should refuse to add and do removal only.

Summary of desired enhancement
Consider this further and document this philosophy