Review and fix leftover CLI references after package split

[fopina]

Summary

There are still a few leftover references to the old [cli] extra and in-repo CLI docs/module paths after moving the CLI packaging to packages/cli/.

Examples

• defectdojo_api_generated/cli/__main__.py still tells users to install defectdojo-api-generated[cli]
• docs/cli.md still documents uv tool install 'defectojo-api-generated[cli]' and imports defectdojo_api_generated.cli.commands.cli
• mkdocs.yml still exposes cli.md in the docs nav
• tests still reference docs/cli.md and the in-package CLI module paths

Why this matters

The repository now treats the main package as library-only, while the CLI is published from the separate wrapper package under packages/cli/. Leftover references make the install story inconsistent and risk broken docs or stale guidance.

Suggested scope

• Audit the repo for stale references to [cli], docs/cli.md, and any outdated assumptions about where CLI packaging lives
• Decide which runtime/module references are still intentional versus leftovers from before the split
• Update docs/messages/tests to consistently point users to the wrapper package (defectdojo-api-generated-cli) where appropriate
• Remove or rewrite obsolete docs/navigation if docs/cli.md is no longer the intended source of truth

Acceptance criteria

• No user-facing install/help text points to defectdojo-api-generated[cli]
• Documentation and nav match the current CLI packaging approach
• Tests reflect the intended CLI docs/module layout
• Any remaining defectdojo_api_generated.cli.* references are deliberate and documented