The “well-known” folder is automatically created by cPanel in order to validate your domain for AutoSSL purposes. AutoSSL is an added feature of cPanel/WHM which offer you free SSL certificate for your domains, its also known as self-signed SSL certificate. The folder .well-known created while the time of the domain validation process as a part of AutoSSL installation.
It is safe to remove the folder if you want, however when the certificate is renewed every 90 days the folder will be re-created.
The readme files change rarely and do not include any kind of change log. Perhaps in the past they included release specific info but not any more. Therefore I don’t think you need to worry about keeping old ones.
I think the auto updater mechanism is to delete and replace the phpList folder. Therefore it’s not currently possible to replace files individually (and leave behind particular files). I believe this is the same concept used by other Open Source Web apps like Nextcloud.
@jimlongo happy to hear that you had a smooth upgrade. Regarding some dot files, it’s actually something that is in future development plans to ignore them. The only directory that is not overwritten during the update is the config folder since everything else can be changed in future releases.
If you have made changes to the files, a backup of the files is recommended,
@jimlongo If it is possible to edit them in the UI, then that is a better means of doing it in as much as those translations will be stored in the database and not overwritten even if all application files are.
However it may be possible to check if the MD5 hash of those files indicates they have been modified, and stop the upgrade if it is detected that they have. That way you could not lose changes that you’ve manually applied. Would such a compromise work for you?