Default "refresh" to False in pkg.upgrade (apt)

This fixes #3300. Also made pep8 fixes. python-mode FTW!
Fix #3300

Per @thatch45, pkg.upgrade will still default to refresh=True, but
list_upgrades will gain a "refresh" argument (which will also default to
true). This behavior will become the new default when #3210 is
implemented.
Merge pull request #3302 from archtaku/issue3300

Add "refresh" to pkg.list_upgrades (apt)