Issue bot quickfix: keep file-specific errors with non-ignorable exception as file-specific errors

Broken since aa92113

Author: ondrejmirtes

src/Command/AnalyseCommand.php

@@ -331,6 +331,7 @@ protected function execute(InputInterface $input, OutputInterface $output): int
 		}
 
 		$internalErrors = [];
+		$internalFileSpecificErrors = [];
 		foreach ($analysisResult->getInternalErrorObjects() as $internalError) {
 			$internalErrors[$internalError->getMessage()] = new InternalError(
 				$internalError->getTraceAsString() !== null ? sprintf('Internal error: %s', $internalError->getMessage()) : $internalError->getMessage(),
@@ -345,6 +346,8 @@ protected function execute(InputInterface $input, OutputInterface $output): int
 				continue;
 			}
 
+			$internalFileSpecificErrors[] = $fileSpecificError;
+
 			$message = $fileSpecificError->getMessage();
 			$metadata = $fileSpecificError->getMetadata();
 			if (
@@ -424,7 +427,7 @@ protected function execute(InputInterface $input, OutputInterface $output): int
 
 		if (count($internalErrors) > 0) {
 			$analysisResult = new AnalysisResult(
-				[],
+				$internalFileSpecificErrors,
 				array_map(static fn (InternalError $internalError) => $internalError->getMessage(), $internalErrors),
 				[],
 				[],