Restored "Cleaned-up invalid edges from duplicate nodes. #6143"

[PawelWMS]

This reverts commit cae9dd7.

Merge Checklist

All boxes should be checked before merging the PR (just tick any boxes which don't apply to this PR)

• The toolchain has been rebuilt successfully (or no changes were made to it)
• The toolchain/worker package manifests are up-to-date
• Any updated packages successfully build (or no packages were changed)
• Packages depending on static components modified in this PR (Golang, *-static subpackages, etc.) have had their Release tag incremented.
• Package tests (%check section) have been verified with RUN_CHECK=y for existing SPEC files, or added to new SPEC files
• All package sources are available
• cgmanifest files are up-to-date and sorted (./cgmanifest.json, ./toolkit/scripts/toolchain/cgmanifest.json, .github/workflows/cgmanifest.json)
• LICENSE-MAP files are up-to-date (./SPECS/LICENSES-AND-NOTICES/data/licenses.json, ./SPECS/LICENSES-AND-NOTICES/LICENSES-MAP.md, ./SPECS/LICENSES-AND-NOTICES/LICENSE-EXCEPTIONS.PHOTON)
• All source files have up-to-date hashes in the *.signatures.json files
• sudo make go-tidy-all and sudo make go-test-coverage pass
• Documentation has been updated to match any changes to the build system
• Ready to merge

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Summary

Re-applying #6143 to get ready for the next release.

Change Log

• Re-applied Cleaned-up invalid edges from duplicate nodes. #6143.

Does this affect the toolchain?

No.

Associated issues

• Cleaned-up invalid edges from duplicate nodes. #6143
• Reverted "Cleaned-up invalid edges from duplicate nodes. #6143" #6288

Test Methodology

• Done in Cleaned-up invalid edges from duplicate nodes. #6143.