Ppa handling bugfix / Apt Sources fixes

PPA and general apt sources fixes bundled in here.

These fixes should address: #4340 , #4268 , and #4433 , as well as other concerns brought up in #4021 .

Please check that everything works as expected.

Known bug: Keys will not be updated unless another change is added (this is due to the way apt handles sources lines. I'll look into this separately.