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.xml – a manual change could break your system in subtle ways.