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It warns also on system headers, even if the user does not want warnings in system headers. The user cannot insert NOLINT suppressions in these headers. Perhaps this is a deeper bug in ClangDiagnosticsConsumer ?
If there is inconsistency, most of the times one wants to change the implementation, not the header, which is likely shared among many other translation units, which would then have to also be changed accordingly, creating code churn. Such a change in a header needs to be a careful design decision, not a change suggested by a linter.