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The app/etc/config.php file contains a list of all the modules in Magento that have been enabled/disabled. It’s also the master list for module ordering – i.e. Magento references this file when deciding what order to load configuration files in.
The order of modules in app/etc/config.php is, itself, determined by the <sequence/> tags in the module.xml files. Magento will rejigger the order of things in app/etc/config whenever you enable a module. This means manual edits to this file will not obey the sequence tags. Since Magento’s configuration loading takes it sort order from app/etc/config.php – a manual change could break your system in subtle ways.