Gulp.js, keep the original folder structure, for side by side compilation.

gistfile1.js

var coffee = require('gulp-coffee');
var eventStream = require('event-stream');
var gulp = require('gulp');
var gutil = require('gulp-util');

var scriptsDirs = [
  'bower_components/este-library/este/',
  'client/',
  'server/'
];

gulp.task('coffee', function() {
  var streams = scriptsDirs.map(function(dir) {
    return gulp.src(dir + '**/*.coffee')
      .pipe(coffee().on('error', gutil.log))
      .pipe(gulp.dest(dir))
  });
  return eventStream.concat.apply(eventStream, streams);
});

Even better:

gulp.task 'coffee', ->
  gulp.src changedFile ? paths.coffee, 'base': '.'
    .pipe plumber()
    .pipe coffee bare: true
    .on 'error', (err) -> gutil.log err.message
    .pipe coffee2closure()
    .pipe gulp.dest '.'

++ This was great thank you for posting!