I've been playing with sfepy for somedays, but still confused about what file/folder does what. 
My proposal is, there can be two top level  folder inside the sfepy source folder => sfepy folder and setup folder.
just like-

/sfepy-2011.2/ -- (extracted sfepy source folder)

/sfepy-2011.2/setup/ -- (inside will be doc folder, setup+license folder, example folder, tests folder - total four (4) folder)

/sfepy-2011.2/sfepy/ -- (inside will be input folder, sfepy program folder, output folder- total three (3) folder)

input folder will be for both the problem definition file+mesh file (input file and mesh file must have to reside in the same folder, in this case its input folder or anywhere in the hard disk), and the file name of both the problem definition file+mesh file will be same, so that sfepy can automatically load the mesh file once the input file has been loaded.

in this way, the main sfepy program can be kept simple and easy to understand & use for advanced users. The setup folder will help the new comers to learn and exercise, and slowly move on to sfepy folder for advanced use.

let me know what do you think.

cheers!