How can I let Ionic know about the change of the project structure?

I have changed the internal "www" folder structure, i.e., moved "scss" folder to a folder "assets", created an "app" folder, etc. Now, when I am trying to run:

ionic setup sass (http://ionicframework.com/docs/cli/sass.html),

it creates a "css" folder in "www" but not "www/assets".

How can I update Ionic on structural changes? I have managed to update ".bowerrc" so it knows where to put packages, but it is only Bower that is aware of the new project structure.

"www" Structure

You can use whatever folder you want for your css files.
One thing you have to change is the gulp task in the gulpfile.js:

gulp.task('sass', function(done) {
  gulp.src('./scss/ionic.app.scss')
    .pipe(sass({
      errLogToConsole: true
    }))
    .pipe(gulp.dest('./www/css/'))
    .pipe(minifyCss({
      keepSpecialComments: 0
    }))
    .pipe(rename({ extname: '.min.css' }))
    .pipe(gulp.dest('./www/css/'))
    .on('end', done);
});

As you can see it transforms the scss file ionic.app.scss in the destination folder ./www/css/ 

.pipe(gulp.dest('./www/css/'))

That's the bit of code you have to change with the new path.

Don't forget to change your index.html with the new path as well:

You don't have to change the ionic.project file as it already includes all the files in the www folder (and subfolders) excluding www/lib (and subfolders); see ref:

LiveReload

By default, LiveReload will watch for changes in your www/ directory, excluding www/lib/.