is there another time war going on? has the the last great time war not finished yet?...

the doctor has been "at war" several times with several different species across time, daleks, sontarans, cybermen etc all of whom showed up to lock him in the pandorica. I think SM's line abou resting the daleks is a big red herring becuase i think what this whole story arc is leading to is the re-establishment of gallifrey and to do that they have to overcome the daleks who i think could possible be behind this whole thing otherwise why go to all the trouble of recreating them in series 5 then do nothing with them. Are we heading towards this?

Thin-gay-Anglican-marine said that it was odd for Lorna Bucket to be in the clerics because her home world was "heaven neutral", which may have something to do with it.

Madame Kovarian goes on to say "our war against you, Doctor", or words to that effect.

The endless bitter war was the war they thought they were fighting against the Doctor, even though the Doctor seemed to be unaware of it.

Or at least not aware of it yet. Maybe his response to this looks like a war, and some of it happens before this episode, so they each think the other started it.

If Madame K is working with the Silents then by the 51st Century it is a rather long war.

20th Century The Doctor attacks The Silence by having every human kill them on sight.
3000 years of The Silence fighting a war with Humanity.
51st Century The Silence counterstrike by creating a weapon to kill the Doctor.

I know that Omega won't be returning as rumoured, but I must say, a human child with Time Lord DNA, being used as a weapon?
That made me think of him