Normally these are kept in var/cache, var/log and var/sessions.
On the develop vagrant machine these are moved to /dev/shm/elewant/var/cache, /dev/shm/elewant/var/logs and /dev/shm/elewant/var/sessions.
Moving them out of the synced folder (and into a shared memory disk) greatly improves performance.
eventstore:herd:purge
This removes all the events in the eventstore. Handy if you want to remove all the herds.
projection:herd:rebuild
This truncates the herd and elephpant tables, and rebuilds them by running all the events in the eventstore again. Handy if you are working on the projections and want to check your work
The Vagrantbox is set up with XDebug, ready to connect to your favorite IDE (I'm guessing that's PHPstorm). All you need to do is install an XDEBUG browser plugin, and set PHPStorm to listen to incoming connections.
If you want to debug a console command, or one of the tests maybe, then you can use a convenient alias:
phpd bin/console
phpd vendor/bin/phpspec run