Clean up GDK in a box documentation

What does this merge request do and why?

Follow up to: !3583 (merged), mostly to fix broken numbered lists because of incorrect indentation of code blocks.

• Before: https://gitlab.com/gitlab-org/gitlab-development-kit/-/blob/dbe8c0772630b68ed256252b5f2ee43c4c918ff2/doc/build_gdk_in_a_box.md
• After: https://gitlab.com/gitlab-org/gitlab-development-kit/-/blob/1897126ffbfd290c58b0c817caa190e9cfbdd692/doc/build_gdk_in_a_box.md

Impacted categories

The following categories relate to this merge request:

• gdk-reliability - e.g. When a GDK action fails to complete.
• gdk-usability - e.g. Improvements or suggestions around how the GDK functions.
• gdk-performance - e.g. When a GDK action is slow or times out.

Merge request checklist

• This change is backward compatible. If not, please include steps to communicate to our users.
• Tests added for new functionality. If not, please raise an issue to follow-up.
• Documentation added/updated, if needed.
• Announcement added, if change is notable.
• gdk doctor test added, if needed.
• Add the ~highlight label if this MR should be included in the CHANGELOG.md.