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I was taking a look at the vu pdf that comes with ps2 linux and I am a little bit uncertain about how it should be used. I couldn't see any way of constructing a gifTag from inside the vu. Is there an easy way to do this, or are you supposed to generate the gifTag and gif packet from the EE then send it to the vu to be modifed in some way (like doing a translation or adding lighting)?

I generate the gifTag on the ee and send it to the vu along with pre-transform and lit geometry(vertices, normals and texcoords). VU code simply makes sure that after all processing is done, the body of the packet (transformed and coloured points) lie in vu memory after the tag (or a copy of it) and kicks that to the GS.
You shouldnt need to touch/modify the tag from vu, since on the ee you know how many points/tris and all that stuff that goes into the tag.