Improve dockerignore support

[jossemarGT]

Improves over #606 which was intended to fix #545.

Currently, we only filter what comes in src array which might unexpectedly let pass files within directories. Also, it removes the need for fs.readFileSync.

BTW I felt the need to update the Vagrantfile but I don't have any strong feeling about dropping that commit if required, since it is outside of the problem I want to address here.