In the config.ini.php, it is not possible to set a configuration settings in a config file without setting the whole category in this config file.
We should have some sort of merging that would make possible to set only a sub configuration variable from the global.ini.php into the config.ini.php. This way, during an upgrade, we could keep only the config/config.ini.php and overwrite the other config files with the updated piwik version and we would keep the user changes.
In config.ini.php it is NOT YET possible to change only value1 doing something like
Currently the user has to paste the whole category to change only this variable
Solution: we should merge the config file before reading them using parse_ini_file?
fixed and added test in 930