I am using vagrant box for developing the project on Symfony (puphpet.com). Locally my webroot files folder mounted at /home/ygerasimov/vagrant/puphpet/puphpet.
In order to debug the project in NetBeans we need to set up folders mapping:
Server path: /var/www/puphpet -- this is folder on the vagrant box where my site is
Project path: /home/ygerasimov/vagrant/puphpet/puphpet -- this is where project folder is mounted on my local machine (host)
Further reading about setting up NetBeans path mapping https://blogs.oracle.com/netbeansphp/entry/path_mapping_in_php_debugger