CSSCat does not copy the files into a new directory before processing. The following snippet shows how to use use CSSCat's fs-helper.js in your build.js file to create a copy of the original directory.

build.js

!function() {
    
    var path = require( 'path' )
        , csscat = require( 'csscat' )
        , fsh = require( 'csscat/lib/fsh' )
        ;
    
    // The directory to copy (relative to this file)
    var original = './';
    
    // The base directory (relative to this file)
    var dir = '../app-build';
    
    // Resolve to absolute paths (relative to this file's directory)
    original = path.resolve( __dirname, original );
    dir = path.resolve( __dirname, dir );
    
    // Delete destination directory
    if ( fsh.exists( dir ) ) fsh.rm( dir );

    // Copy the target directory to the destination directory
    console.log( '\nCopying files to the destination directory at "' + dir + '"');
    fsh.copyDir( original, dir );

    // Now that the we have fresh copy, let's get busy on it
    csscat.init({
        dir: dir
    });
    
}();