1. In the Terminal of the original Matomo app instance, run this command: mysqldump -h${CLOUDRON_MYSQL_HOST} -u${CLOUDRON_MYSQL_USERNAME} -p${CLOUDRON_MYSQL_PASSWORD} --single-transaction --routines --triggers ${CLOUDRON_MYSQL_USERNAME} > /tmp/matomo-mysqldump.sql
2. Download from the /tmp directory the matomo-mysqldump.sql file.
3. Deploy a new instance of Matomo (on a new domain of course for now)
4. Put the new instance of Matomo into Recovery Mode and then enter the Terminal and run this command to clear out the database (a clean start): mysql --user=${CLOUDRON_MYSQL_USERNAME} --password=${CLOUDRON_MYSQL_PASSWORD} --host=${CLOUDRON_MYSQL_HOST} ${CLOUDRON_MYSQL_DATABASE} -Nse 'show tables' | while read table; do mysql --user=${CLOUDRON_MYSQL_USERNAME} --password=${CLOUDRON_MYSQL_PASSWORD} --host=${CLOUDRON_MYSQL_HOST} ${CLOUDRON_MYSQL_DATABASE} -e "SET FOREIGN_KEY_CHECKS = 0; drop table $table"; done
5. Upload the matomo-mysqldump.sql file that had been downloaded from step 3 above to /tmp directory on new Matomo instance, then run this command to import the database: mysql --user=${CLOUDRON_MYSQL_USERNAME} --password=${CLOUDRON_MYSQL_PASSWORD} --host=${CLOUDRON_MYSQL_HOST} ${CLOUDRON_MYSQL_DATABASE} < /tmp/matomo-mysqldump.sql
6. Restart the app instance. Test, and then move old Matomo instance to a new domain, and put new Matomo instance on old domain so that website analytic agents don't need to be updated to any new domain. Adapt to your needs as necessary though.

1. In the Terminal of the original Matomo app instance, run this command: mysqldump -h${CLOUDRON_MYSQL_HOST} -u${CLOUDRON_MYSQL_USERNAME} -p${CLOUDRON_MYSQL_PASSWORD} --single-transaction --routines --triggers ${CLOUDRON_MYSQL_USERNAME} > /tmp/matomo-mysqldump.sql
2. Download from the /tmp directory the matomo-mysqldump.sql file.
3. Deploy a new instance of Matomo (on a new domain of course for now)
4. Put the new instance of Matomo into Recovery Mode and then enter the Terminal and run this command to clear out the database (a clean start): mysql --user=${CLOUDRON_MYSQL_USERNAME} --password=${CLOUDRON_MYSQL_PASSWORD} --host=${CLOUDRON_MYSQL_HOST} ${CLOUDRON_MYSQL_DATABASE} -Nse 'show tables' | while read table; do mysql --user=${CLOUDRON_MYSQL_USERNAME} --password=${CLOUDRON_MYSQL_PASSWORD} --host=${CLOUDRON_MYSQL_HOST} ${CLOUDRON_MYSQL_DATABASE} -e "SET FOREIGN_KEY_CHECKS = 0; drop table $table"; done
5. Upload the matomo-mysqldump.sql file that had been downloaded from step 3 above to /tmp directory on new Matomo instance, then run this command to import the database: mysql --user=${CLOUDRON_MYSQL_USERNAME} --password=${CLOUDRON_MYSQL_PASSWORD} --host=${CLOUDRON_MYSQL_HOST} ${CLOUDRON_MYSQL_DATABASE} < /tmp/matomo-mysqldump.sql
6. Restart the app instance. Test, and then move old Matomo instance to a new domain, and put new Matomo instance on old domain so that website analytic agents don't need to be updated to any new domain. Adapt to your needs as necessary though.

Errors below may be due to a partial or failed upload of Matomo files.
--> Try to reupload all the Matomo files in BINARY mode. <--

Missing file: /app/code/misc/user/index.html

Does anyone else see that message too in the System Check, or is it just me again? lol

Here's what's in the directory when I check in on it (it's definitely missing the index.html file):

root@b11704ef-8d66-4b9c-a43b-57483d5ce25b:/app/code/misc/user# ls -alh
total 96K
drwxr-xr-x 2 www-data www-data 4.0K Nov 27 02:52 .
drwxr-xr-x 3 www-data www-data 4.0K Nov 27 02:52 ..
-rw-r--r-- 1 www-data www-data 1.2K Nov 28 05:41 .htaccess
-rw-r--r-- 1 www-data www-data 1.4K Nov 27 02:52 favicon.png
-rw-r--r-- 1 www-data www-data 9.3K Nov 27 02:52 logo-header.png
-rw-r--r-- 1 www-data www-data  65K Nov 27 02:52 logo.png

However good to know: one instance has a database of 1.2G and it took quite some time (I guess 3 minutes on a 10 core/68GB) to update/convert the database. In the meanwhile the instance showed only a warning page that the database needs to be updated while it was actually already busy. I "knew" that because it was the second instance and the update/conversion of first instance (much smaller) went fine.

It seems that 4.0.0 may need a new directory created that doesn't yet exist and since it's in app/code it's not able to create it either.

The /app/code/tmp is already symlinked to /run/matomo/tmp. I checked a new install and it had this directory created (by matomo). Also, our cloudron.io, matomo instance updated fine as well. I also deleted tracker directory and restarted the app. Matomo creates that directory again.

Do you have the logs before this error message? Would be good to know where in the start up script it fails.

/tmp reference should be configured appropriately.