Clandestine is still disputed; there is enough stuff in Clandestine, as Joyce put it "to keep the critics busy for a hundred years" (although i believe he was talking about his own work at the time). Most attention surrounds the box and what it represents. I believe it represents dignity, or something similar. Davey kisses a stranger at the cafe, and thereby loses the box (his dignity), similarly, Adam wins dignity in a game of cards, but it falls apart in his hands when he leaves, symbolising that it was false dignity, and his opponents left with the real dignity. At the end of Clandestine they open the box, but we do not see inside - interestingly, Bleed Black - track 3 on Sing the Sorrow - opens with the lyrics "I am exploring the inside, I find it desolate". If we make the link between Clandestine and STS, we can deduce not only that the box was empty, but that STS "starts" at the end of Clandestine, and "starts" on track 3, not 1. We then discover that running the CD in that order (i.e. 3, 4, 5, 6 ,7 , 8, 9, 10, 11, 12, 1, 2.) puts the Leaving Songs in their correct order. However, the significance of this has never been found. There was a lot of twaddle circulating at one point about the whole album being about a cycle of life, death and resurrection, but i dont buy into it.
I'm sorry for the length but, as I said earlier, it is a very complex matter :)