Em vez de file:///path/to/repo
:
deb "file:///media/miguel/My Passport/xenial-repo" xenial main restricted universe multiverse
...
Deve ser apenas file:/path/to/repo
, no seu caso:
deb "file:/media/miguel/My Passport/xenial-repo" xenial main restricted universe multiverse
deb "file:/media/miguel/My Passport/xenial-repo" xenial-backports main restricted universe multiverse
deb "file:/media/miguel/My Passport/xenial-repo" xenial-updates main restricted universe multiverse
deb "file:/media/miguel/My Passport/xenial-repo" xenial-proposed main restricted universe multiverse
deb "file:/media/miguel/My Passport/xenial-repo" xenial-security main restricted universe multiverse
Para mais informações sobre o assunto, Como criar repositórios pessoais .