Remove vagrant directory

Move all Vagrant related files to the top directory (acceptance), to
keep all the needed files under the same directory.
Refactor VM folders structure

- Don't use a shared folder for services, ensure it's in /vagrant, and
  create a symbolic link in ~/clara/ instead.
- Don't use a shared folder for logs, create a new directory inside the
  services directory.
- Put the Clara sources in ~/clara/dev
Ensure list of packages is updated

For some reason, Ubuntu repositories like to remove old version of
packages. If the list of packages is not updated, it will likely
generate an error when trying to provision the machine.

Fix with a shell script provisioner that will run before Puppet. This
script will execute `apt-get update` when the machine is created. Then,
it will run the command again only if the list has not been updated in
one week.
Require python-zmq before running clara-manager