Geo: Part 1 of Enforce not null packages_package_files.file_store

What does this MR do?

Part of #229412 (closed):

When sync_object_storage is false, RegistryConsistencyService calls methods which use the clause WHERE file_store = 1. We need to:

• index that field (which we've done).
• make it non-nullable.
  • So we don't have to add OR file_store IS NULL to ensure we process all records. That OR harms performance (see the performance improvement when we removed this clause from LFS objects).

• Copy !38549 (merged) but for packages_package_files.file_store
• Copy !38719 (merged) but for packages_package_files.file_store (I marked it dependent on this one since it's not merged the time of this writing)

Migration output

Does this MR meet the acceptance criteria?

Conformity

• Changelog entry
• Documentation (if required)
• Code review guidelines
• Merge request performance guidelines
• Style guides
• Database guides
• Separation of EE specific content

Availability and Testing

• Review and add/update tests for this feature/bug. Consider all test levels. See the Test Planning Process.