Magento-actions may need to run composer install which will override some files outside of the vendor folder in a magento project.
For example, you may have had manually modified the app/bootstrap.php file or the index.php. These modifications will be overridden by magento default files during the composer installation process. To prevent this please modify your composer to discard the overriding as such:
{
"extra":{
"magento-force": true,
"magento-deploy-ignore": {
"*": ["/app/bootstrap.php"]
}
}
}