Lots of suggestions:
* Don't write your own cron scripts, use Symfony Commands.
* Delete the Acme Bundle.
* Don't store your vendor directory in Git! Completely unnecessary and waste of 47MB.
* Don't commit parameters.yml, that's what parameters.yml.dist is for.
* Use a migration tool (Doctrine Migrations are fine) instead of one big SQL dump.
* Not sure what mongodb/example.php is for.
* Why is all the plivo stuff in web/plivo/ instead of being a callable controller?
* Are you manually generating your Doctrine entities?
* Don't commit your asset directories (they should be symlinks).
* No need to use PHPMailer (or include the entire project in your repository), Symfony comes with Swiftmailer which is great.
* Same with src/Phone, add that library through Composer (https://packagist.org/packages/practo/libphonenumber-for-php).
The design looks great, but I wouldn't trust a lot of this (especially after seeing how many hosts and usernames and passwords you left scattered about).