I'd like to use redshift on Ubuntu to redshift all but some whitelisted set of applications, e.g. Emacs, which I've configured to look the way I want already. Is this possible? If so, how do I specify the applications?
I don't think so, the only thing I saw was that you can start it with ...
(with some options) and disable it with ...
pkill -USR1 redshift
That seem to indicate there are no config options for enabling/disabling it per started software and that redshift works on a system wide base. The sample configuration does not have anything on it either. Something you might be able to work with: you can enable/disable it per viewport. Maybe you should group the software you do not want to use it with and make them open on viewport 2, and have redshift not do viewport 2.
So when you do
pkill -USR1 redshift && emacs
emacs would start without it and you would have to manually restart redshift. But putting that in front of any software you want it to start without seems a bit much.