Ensure consistency of system flag on IndexMetadata after diff is applied

[cwperks]

Description

This PR ensures the consistency of the isSystem flag between leader and follower after the IndexMetadataDiff is applied when computing new cluster state.

This inconsistency can appear during rolling upgrades if nodes of a new version know of an index as a system index, but nodes of a previous version treat the same index as a regular index. For example, if a plugin retroactively declares an index to be a system index through SystemIndexPlugin.getSystemIndexDescriptors (Example PR) there can be a discrepancy in the IndexMetadata (for the same version) between the cluster manager node and other nodes in the cluster.

The reason this happens is because when the IndexMetadataDiff is applied, its taking the value from the previous metadata on the node instead of the new metadata that it has received from the incoming publishRequest. As a result, the diff here is being computed incorrectly. It should take the value from the diff instead of from the previous index metadata.

Related Issues

Resolves https://github.com/opensearch-project/OpenSearch/issues/16643

Check List

• [ ] Functionality includes testing.
• [ ] API changes companion pull request created, if applicable.
• [ ] Public documentation issue/PR created, if applicable.

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[github-actions[bot]]

:white_check_mark: Gradle check result for b526a45b5155135184990d711c92d31d9befe736: SUCCESS

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 72.19%. Comparing base (05513df) to head (76bde0e).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #16644 +/- ## ============================================ + Coverage 72.11% 72.19% +0.07% - Complexity 65230 65299 +69 ============================================ Files 5318 5318 Lines 303915 303915 Branches 43975 43975 ============================================ + Hits 219180 219421 +241 + Misses 66813 66544 -269 - Partials 17922 17950 +28 ```

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[owaiskazi19]

@cwperks this change needs a changelog entry

[cwperks]

@cwperks this change needs a changelog entry

Added

[github-actions[bot]]

:white_check_mark: Gradle check result for 7ff0651dd39b8539b34d55001e7658556f8647ab: SUCCESS

[cwperks]

Resolved conflicts in CHANGELOG

[github-actions[bot]]

:white_check_mark: Gradle check result for 76bde0ec9c862402c730528c5cd3982c114b4e1f: SUCCESS