How to add src files in the middle of a pipe

You don’t need to add files to the original src, but rather to use coffee only “if”…

So, use gulp-if

gulp.task('task', function() {
  gulp.src('./stuff/*')
    .pipe(gulpif(/[.]coffee$/, coffee()))
    .pipe(gulp.dest('./dist/'));
});

See here more about gulp-if.