I quote from the Dev Log
There are several fixes to the Updater to make sure updating to Matomo 4.6.2 doesn’t result in the System Check message “Files to Delete”.
But here it is, the message again, mentioning files to delete whereas they are Matomo files which I assume must not be deleted.
Any light upon this?
Can you list the files here?
matomo-archive-output.log
misc/others/uninstall-delete-piwik-directory.php
package-lock.json
phpcs.xml
vendor/php-di/php-di/.gitstats.yml
vendor/php-di/php-di/.phpstorm.meta.php
vendor/twig/twig/.php_cs.dist
The list of files keep growing. Does anyone have a solution?
config/environment/test.php
config/environment/ui-test.php
matomo-archive-output.log
misc/others/uninstall-delete-piwik-directory.php
package-lock.json
phpcs.xml
node_modules/chroma-js/.npmignore
node_modules/iframe-resizer/.ncurc.json
node_modules/iframe-resizer/.prettierrc
node_modules/jquery.browser/.npmignore
node_modules/jquery.scrollto/.jscsrc
node_modules/jquery.scrollto/.npmignore
node_modules/ng-dialog/.npmignore
node_modules/qrcodejs2/.npmignore
vendor/matomo/device-detector/.yamllint
vendor/php-di/php-di/.gitstats.yml
vendor/php-di/php-di/.phpstorm.meta.php
vendor/twig/twig/.php-cs-fixer.dist.php
vendor/twig/twig/.php_cs.dist
How did you install and update Matomo?
And which is your current version, now?
hello, I have On Premise, installed it several months ago and always updated through the dashboard as new versions came along (so now it’s at 4.7.1)
I am standing by looking forward to any feedback 
Actually manually deleting those files should fix it.
We had an issue in older version, that prevent files starting with . being deleted. Which explains most entries in the list. In addition files in the base directory aren’t removed automatically.
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…but are you really sure about that? I mean, files are files, and if they get deleted I guess Matomo will break. Besides, not all have a . prefix
I trust you, but how can I restore Matomo if anything breaks?
All files you mentioned are not needed for Matomo to work ( matomo-archive-output.log is a bit special as it is the output you set up in your cronjob and you should change the cronjob so it doesn’t put the output log into the web directory as this way everyone on the internet can read it).
If something breaks, you can always replace the files with the ones from the latest Matomo download.
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I actually have put matomo-archive-output.log under my home directory but outside my public_html folder.
Thank you for clarifying this matter. I shall contact you again if anything goes wrong.
Sorry to bother again, but I just realized that there’s a new copy of that file generated every day. Is there not a possibility to have it stored in the same location automatically?
The file is put at the path you specified in your cron setup (the > /home/example/matomo-archive.log part)
See https://matomo.org/docs/setup-auto-archiving/ for more information.
I have a Wordpress site, and your tutorial says I shouldn’t do anything then.
On the other hand, I have noticed that I had set a Cronjob
Should I just edit those, like /home/agenda/console core:archive, i.e. removing the domain where I have Matomo installed?
You don’t need to edit the actual command, but just the part in the end where you redirect (>) the output into a file. Just redirect it to another file outside the public directory.
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I don’t really know what’s happening here.
I keep getting Cron Daemon homedir/matomo-archive-output.log emails saying that /usr/local/cpanel/bin/jailshell: /opt/cpanel/ea-php73/root/usr/bin/php: No such file or directory
yet we discussed about removing that file.
I now also have a red alert in diagnostics mentioning that the last archive was successfull (so why the red alert?), asking to verify my crontab, which is set correct since my first installation.
I need support from the dev, not users. please