3. Configuration
There are two ways to configure MESS: through configuration files and through command-line arguments. Using a configuration file helps to keep command-line usage simple. You typically only need to specify an input and output file path via the command-line, and maybe select a different configuration file if you're working with different games or mods.
The most important settings are the location of the mess.fgd file, the template entity directories and the template maps directory. By default, MESS will use the folder where MESS.exe is located as the destination for its mess.fgd file, and it will look for a template_maps sub-folder in that folder. Normally this will work fine, but in some cases it's necessary to put mess.fgd in a different folder, such as when working with TrenchBroom.