(please read warning in above comment before following instructions below).
If you want to make config file changes:docker exec -ti mysql /bin/bash Edit /run/mysql/my.cnf as needed supervisorctl restart mysql
It is important to note that the changes to config files are not persistent across container restarts and server reboot. In general, we have not envisioned Cloudron as a development environment, but we do have many devs using it as such. So, if there is interest, maybe we need to improve things for such use cases.