bisect help

I've got a use-case that I can't figure out.  The problem:

- I have a tree with 2.6.17 + changes to make my target board work.
- SATA works as of 2.6.17, but stops working in the libata dev tree.

I want to do a bisect on this to figure out why. I think the problem is that the common ancestor between the two trees is 2.6.17, and when I bisect I don't have any of my arch-specific changes still in the tree (so the kernel doesn't boot, but not for SATA reasons)

I have my tree in "master", Jeff's SATA tree in "satadev". I've tried a few things like:

git checkout -b garbage master git pull . satadev # to get all the sata changes git bisect start git bisect bad git bisect good master

but it seems like this causes the bisect to happen between the common ancestor (v2.6.17) and the merge of master & satadev.

help! thanks mh