I use my functions.php file by including functions from other folders. I do this because of that when users want to edit functions directly I provide them find which function they want to edit.
In template path there are common functions.php file and a folder that storing functions. I call functions in functions.php from folder which named functions using require_once(TEMPLATEPATH.'/functions/function-name.php');
Storing functions isolated folders is suitable for WordPress template developing? Should I store whole functions in common functions.php or seperated?