fix: refactor index_together to indexes for Django 5.2 support (II)

[UsamaSadiq]

Description

• For adding Django 5.2 support under the issue Django 5.2 Upgrade public-engineering#339, refactored the index_together to indexes as per the discovery done in the issue Deprecate Model.Meta.index_together in favour of Model.Meta.indexes public-engineering#343
• The table grades_persistentcoursegrade has around ~66M records in 2U/edX db
• The rawsql generated for this change is following (old_index representing the previous unnamed index) :

ALTER TABLE `grades_persistentcoursegrade` RENAME INDEX `old_index` TO `passed_timestamp_course_id_idx`;

ALTER TABLE `grades_persistentcoursegrade` RENAME INDEX `old_index` TO `modified_course_id_idx`;

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2U Release Notice: This PR has been deployed to the edX staging environment in preparation for a release to production.

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2U Release Notice: This PR has been deployed to the edX production environment.