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To upgrade the module, simply upload the new module archive.
The Starting with version 2.0 the settings are managed through the module setting pages. All settings will be automatically migrated upon updating the module.
After you have uploaded the new files, you can optionally remove the files "customconfig.php", "licensekey.php", "classes.php", "functions.php" from the /modules/servers/dedicated/ directory.
To complete the upgrade, follow the normal installation guide.