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The problem was caused by the discrepancy in Qodana configurations between the main branch and feature branches from the pull requests.
When analyzing pull requests, Qodana by default runs the analysis on the changed files first from the target branch, and then on the same files from the source branch, so it can use an unexpected configuration.

If you want to test out a new Qodana configuration on a separate branch, we recommend first running Qodana analysis on it using the workflow_dispatch trigger on the branch. This way Qodana run full scan on the specified branch and will apply Qodana configuration from that branch.

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@mridang
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@brichbash
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@mridang
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@brichbash
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Answer selected by brichbash
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