extra/vm/setup.sh: Install `lsof`

Used by `extra/runner/run` since commit 313cf4fa. `lsof` is already
installed as a dependency of `ubuntu-standard`, but it is nice to list
it explicitly so that this list of packages can serve as documentation
to people who want to build their own stb-tester packages for Ubuntu
or other operating systems.

`lsof` isn't in `extra/stb-tester.spec` because that package doesn't
install the runner; for now the runner is only available from the source
repository.
extra/vm/setup.sh: Document why each package is needed

This information was available in the commit message that introduced
each line, but it's probably unreasonable to expect people to look up
that information with `git annotate`.