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Update file references again
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@ -291,6 +291,7 @@ class Analyzer
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$codebase->file_reference_provider->setAnalyzedMethods($this->analyzed_methods);
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$codebase->file_reference_provider->setFileMaps($this->getFileMaps());
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$codebase->file_reference_provider->setTypeCoverage($this->mixed_counts);
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$codebase->file_reference_provider->updateReferenceCache($codebase, $scanned_files);
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if ($codebase->diff_methods) {
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$codebase->statements_provider->resetDiffs();
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