There is no reason to build a configuration file of duplicate settings. The user can acquire the defaults from the config section and only inject the changes into the game section.
This adds support for separate config and data dirs.
On Linux, these will be compliant XDG Basedir Specification, i.e.
XDG_CONFIG_HOME and XDG_CONFIG_DIRS (or XDG_DATA_HOME and XDG_DATA_DIRS
respectively). On all other platforms, there currently just set to the
homedir path (so no previous behaviour has been changed).
If reicast wants to read and write a data file, it just calls
get_data_path("/samplefile.txt"). If it does not need to write to
that file, it just uses get_data_path("/samplefile.txt", false). That
way, we can also use system-wide dirs (like /usr/share/reicast on
linux), that the user usually doesn't have write access to.
The same applies for config file, where you use get_config_path(args)
respectively.