A workaround to be able to create the maps files into a separate file of the javascript files from the coffescript files what are into a tree structure.

file-tree.txt

project
  src
    coffee
      foo.coffee
      component
        bar.coffee
      animals
        dog.coffee
        cat.coffee
  public
    scripts
      foo.js
      maps
        foo.js.map
      component
        bar.js
        maps
          bar.js.map
      animals
        dog.js
        cat.js
        maps
          dog.js.map
          cat.js.map

gulpfile.js

var gulp        = require('gulp');
var $plugin     = require('gulp-load-plugins')({ camelize: true});
var gutil       = require('gutil');
var glob        = require('glob');
var path        = require('path');

/**
 * Project Paths
 */
glob.paths = {
  publicScript:    './public/scripts/',
  srcCoffee:       './src/coffee/'
};

/**
 * Create the javascript and map files from the coffeescripts
 */
gulp.task('coffee-map', function( callback ) {

  // // this what we want to do, but doesn't work as excepted //
  // gulp.src(glob.paths.srcCoffee + '**/*.coffee')
  //   .pipe($plugin.sourcemaps.init())
  //   .pipe($plugin.coffee({bare: true}).on('error', gutil.log))
  //   .pipe($plugin.sourcemaps.write( './maps/'))
  //   .pipe(gulp.dest(glob.paths.publicScript));

  /**
   * @workaround This is a not so easy or fast way to compile the coffee
   * scripts and create the maps but it was necessary to the current version
   * @todo use the tradicional way when fixed
   * @link https://github.com/gulpjs/gulp/issues/356
   */
  var coffeeFiles = glob.sync( glob.paths.srcCoffee + '**/*.coffee');
  var intCounter = 0;
  coffeeFiles.forEach(function(fullPathFileName){
    
    var srcDir = path.dirname(fullPathFileName);
    var srcRelativeDir = srcDir.substr(glob.paths.srcCoffee.length);
    var destDir = glob.paths.publicScript + srcRelativeDir + "/";

    var answer = gulp.src(fullPathFileName)
      .pipe($plugin.sourcemaps.init())
      .pipe($plugin.coffee({bare: true}).on('error', gutil.log))
      .pipe($plugin.sourcemaps.write( './maps/'))
      .pipe(gulp.dest(destDir));

    answer.on('end',function(){
      intCounter++;
      if( intCounter >= coffeeFiles.length ) {
        callback();
      }    
  });
 });