-Finally, for some reason, the switch to puppet seems to heavily confuse
-samhain (possibly the config file getting changed out from under it?).
+Double check apt - the puppet setup usually results in duplicate apt
+sources, since we ship a few under sources.list.d. Remove any unnecessary
+entries from sources.list.
+
+We ship a samhain config file that includes /lib and /usr/lib. This will
+almost certainly be different than the config file on the machine, so it
+will result in 1000s of files changed.