@ChristopherMag This should be fixed now with the latest package. I found that we have to set GF_PLUGIN_DIR env var or pass --pluginDir separately for the CLI tool. The server reads configs from custom.ini but the CLI does not (there's probably some good reason for this discrepancy).
Right, /app/data/custom.ini is where the users customizations go. What db were you using in your existing installation? The cloudron package uses postgres. To get the DB connection credentials, you can go to the Terminal of the app and do env | grep CLOUDRON_POSTGRES. You can also click the postgres button on the top and it will paste the CLI needed to access postgres.