Fix virtualbox tests
- Run --list-modules command in VM. Replaces the broken --diagnose command. See freedombox#2076 (closed).
- Ignore errors while cleaning up VM.
- Send shutdown command to VM.
Also includes a minor fix for vagrant-package script.
Tests: Ran tests including VM test. Also built a vagrant box.
Signed-off-by: James Valleroy jvalleroy@mailbox.org