Remove package_registry duplicate indexes

What does this MR do and why?

After #385701 (closed), we can identify duplicated indexes. Currently, many duplicate indexes can be removed from our database, as they are no longer needed.

The list of duplicated indexes can be found in the duplicate_indexes.yml file.

We have identified the following duplicated indexes owned by grouppackage registry:

Duplicated Index	Covered by
index_packages_debian_group_distributions_on_group_id	uniq_pkgs_debian_group_distributions_group_id_and_codename & uniq_pkgs_debian_group_distributions_group_id_and_suite
index_packages_debian_project_distributions_on_project_id	uniq_pkgs_debian_project_distributions_project_id_and_codename & uniq_pkgs_debian_project_distributions_project_id_and_suite
index_packages_tags_on_package_id	index_packages_tags_on_package_id_and_updated_at

This MR is to remove those duplicate indexes.

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Related to #428563 (closed)