Update `gdk cleanup` command to exclude sub-project dependencies

What does this merge request do and why?

This MR updates the logic in Asdf::ToolVersions class to ensure that the gdk cleanup command doesn't remove software listed in sub-projects' .tool-versions files. Previously, only the .tool-versions file in the GDK directory was considered. With this change, the gdk cleanup command will only remove unnecessary software not listed in any .tool-versions file.

Closes #2088 (closed)

How to set up and validate locally

1. git checkout 2088-gdk-cleanup-to-exclude-sub-project-dependencies
2. gdk cleanup

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.