added deepExclude, generateSourceMaps options.

Had to add deep exclude option (true by default). This is useful in a situation where the user may wish to ignore a folder of modules but keep any external dependencies those modules may have, such as jQuery or Knockout.

e.g. 

    gulp.task('durandal', function(){
        return durandal({
                baseDir: 'App',
                main: 'main.js',
                //output: 'main.js', //same as default, so not really required.
                deepExclude: false,
                generateSourceMaps: false,
                almond: false,
                minify: false,
                verbose: false,
                pluginMap: {
                    '.html': 'text',
                    '.json': 'text',
                    '.txt': 'text'
                },
                moduleFilter: function(moduleName){
    				var accept = true;
    
    				if (moduleName.indexOf('apps/') == 0) accept = false;
    				if (moduleName.indexOf('text!apps/') == 0) accept =  false;
    				if (moduleName.indexOf('css!apps/') == 0) accept =  false;
    
    				var action = accept ? "Accepted" :"Skipping";
                	console.log(action + ": " + moduleName);
                	return accept;
                }
            })
            .pipe(gulp.dest('path/to/build'));
    });