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Clarify where to run `gdk init`

What does this Merge Request do?

Clarifying Initialize a new GDK directory section in the set-up-gdk.md.

The phrasing confused me because I didn't know what source code are we talking about. I thougth that I'm supposed to run the gdk init inside of my checked out https://gitlab.com/gitlab-org/gitlab repository.

Merge Request checklist

  • Tests added for new functionality. If not, please raise Issue to follow-up.
  • This change is backward compatible. If not, please include steps to communicate to our users.
  • Documentation added/updated, if needed.
  • gdk doctor test added, if needed.

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