Excluded sources are being processed for mutation

[IonBazan]

Question	Answer
Infection version	0.27.11
Test Framework version	PHPUnit 9.6
PHP version	8.3.6
Platform	e.g. Ubuntu and MacOS
Github Repo	https://github.com/IonBazan/composer-diff

I am using Infection together with PHPUnit in my tool: https://github.com/IonBazan/composer-diff which targets PHP versions 5.3~8.4 so I'm conditionally aliasing some classes depending on PHP version as a polyfill for Symfony 7:
https://github.com/IonBazan/composer-diff/blob/d7f3cd5333c760d5bdfe0178571c99f52979bb9f/src/Command/DiffCommand.php#L15-L24

Since BaseNotTypedCommand remains uncovered when running under PHP 7+, I added it to excludes:
https://github.com/IonBazan/composer-diff/blob/d7f3cd5333c760d5bdfe0178571c99f52979bb9f/infection.json.dist#L2-L9

This used to work perfectly well as the file was completely ignored but recently (unfortunately I'm not able to check when) it started to fail, as the excluded file started to be processed by the mutant generator (tokenized) and crashed.

I temporarily solved it by passing --only-covered flag to avoid this file from being loaded but ideally, files mentioned in excluded should be omitted completely.

The last time it worked was on 29 Dec 2023, if that helps: IonBazan/composer-diff@005967f

Output after passing `--only-covered`

Infection - PHP Mutation Testing Framework version 0.27.11


Running initial test suite...

PHPUnit version: 9.6.15

  175 [============================] 5 secs

Generate mutants...

Processing source code files: 25/25
.: killed, M: escaped, U: uncovered, E: fatal error, X: syntax error, T: timed out, S: skipped, I: ignored

..................................................   ( 50 / 357)
..................................................   (100 / 357)
..................................................   (150 / 357)
..................................................   (200 / 357)
..................................................   (250 / 357)
..................................................   (300 / 357)
..................................................   (350 / 357)
.......                                              (357 / 357)

357 mutations were generated:
     357 mutants were killed
       0 mutants were configured to be ignored
       0 mutants were not covered by tests
       0 covered mutants were not detected
       0 errors were encountered
       0 syntax errors were encountered
       0 time outs were encountered
       0 mutants required more time than configured

Metrics:
         Mutation Score Indicator (MSI): 100%
         Mutation Code Coverage: 100%
         Covered Code MSI: 100%

Output with issue

Infection - PHP Mutation Testing Framework version 0.27.11


Running initial test suite...

PHPUnit version: 9.6.15

  174 [============================] 6 secs

Generate mutants...

Processing source code files: 21/26
Fatal error: Declaration of IonBazan\ComposerDiff\Command\BaseNotTypedCommand::execute(Symfony\Component\Console\Input\InputInterface $input, Symfony\Component\Console\Output\OutputInterface $output) must be compatible with Symfony\Component\Console\Command\Command::execute(Symfony\Component\Console\Input\InputInterface $input, Symfony\Component\Console\Output\OutputInterface $output): int in /Users/ionbazan/work/composer-diff/src/Command/BaseNotTypedCommand.php on line 16