Replace deprecated skip-auto-migrations occurrence

What does this MR do?

Replace all occurrences of skip-auto-migrations with skip-auto-reconfigure.

Related issues

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/45031

Author's checklist

• Apply the correct labels and milestone
• Port the MR to EE (or backport from CE): always recommended, required when the ee-compat-check job fails

Review checklist

• Your team's review (required)
• PM's review (recommended, but not a blocker)
• Technical writer's review (required)
• Merge the EE-MR first, CE-MR afterwards