The Guardian editors did an interview a while ago with Charlie Rose explaining the process[1], and I don't think it's so much an agreement as that they run stories past the government first, for comment, and for the government to give them specific objections to revealing information - so far they've not heard anything concrete, just 'don't publish this' - though this was before the laptop debacle. The Guardian and WaPo redact the documents before publication (sometimes heavily). The Independent is restating that in a slightly misleading way to imply that The Guardian has some sort of firm agreement with the government on vague terms like 'national security'. So I don't think the Guardian needs to clear anything up, they've been quite clear, and even if there were an agreement, I think the Guardian would argue that nothing they have or will publish does endanger 'national security' - it would come down to arguments over the meaning of that term. Does it meant the comfort and ease of our politicians and security services to keep their activities secret, or does it mean actual danger to citizens of the UK?
[1] https://www.youtube.com/watch?feature=player_embedded&v=7pdz...
From the Independent story:
The Independent is not revealing the precise location of the station but information on its activities was contained in the leaked documents obtained from the NSA by Edward Snowden.
This looks really bad for the Independent, as the article makes it sound like this is based on a leak from Snowden, and yet Snowden has specifically denied this, and if you go back and reread the article in that light, it becomes clear that they have simply reproduced a leak at the behest of GCHQ, carefully worded in order to preempt future scoops while giving little away, and yet get in front of the news with their best possible spin. I love the ending as well where they give up pretending to be independent:
Intelligence sources have denied the aim is a blanket gathering of all communications, insisting the operation is targeted at security, terror and organised crime.
We know they already collect it all, and the only limits are technical ones (for GCHQ at least, and it's starting to look like the NSA are similar). We already know they target individuals who are nothing to do with terror and organised crime (Laura Poitras, Appelbaum, Miranda etc).