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Avoid cyclic references during incremental project update
This change operates under the assumption that neither the starting state nor the final state include any cycles. By removing all project references from projects that change their reference sets prior to other work, we ensure extraneous references cannot lead to an invalid intermediate state. This increases the amount of work required to complete an incremental update when project references change, but does not impact the more common updates where all project references are unchanged. Fixes #52578
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