It has been reported that the file named PackageImportList.txt sometime causes user projects to fail on startup, with the following error message :
[Auto Package] : Couldn't find the packages list. Be sure there is a file called PackageImportList in your project
UnityEngine.Debug:LogError(Object)
PackageChecker:CheckPackage()
UnityEditor.EditorAssemblies:processInitializeOnLoadAttributes()
A common workaround is to create a dummy file with an empty list of packages. It would be worth investigating what is causing this file to get deleted in some workflows, and maybe reconsider if the absence of this file should cause a critical error on the project startup.
The issue has been reported on the Unity forums : https://forum.unity.com/threads/couldnt-find-the-packages-list-be-sure-there-is-a-file-called-packageimportlist-in-your-project.534331