I assume from your comments that you're using git not quilt? (since quilt doesn't really care
if you change the tree under it, you just do a quilt pop -a; install new tree; quilt push -a)
The way to develop against linux-next in git is to use git rebase --onto to move your patches
as linux-next changes.
So, assume you have a git tree with your patches on the master branch. You also need to
record the base of your branch with either a tag or a branch (you do this before you start
adding patches) so that git format-patch base produces exactly all the patches you're
managing. The way I set this up is to clone a tree (git clone <tree>) record the base (git
branch base) and simply develop committing along the way.
Now set up remote tracking branches (I tend to do one for linux-next and one for linus as):
git remote add -t master -f linus
git remote add -t master -f next
The point of keeping the linus tree is that eventually all the branches that comprise next are
merged into linus, at which point your patches will be ready for submission against vanilla
To download the current trees of the day, simply do a
git remote update
and to put your patches onto the current linux-next do
git rebase --onto remotes/next/master base
If this is successfully completed, you need to record the fact that you've moved the base of
git branch -M base remotes/next/master
You can keep doing this as many times as linux-next updates.
If you think you're ready to try to place your patches onto vanilla linus, just repeat the
recipe but with remotes/linus/master instead of remotes/next/master. If your attempt to
rebase onto linus fails (usually because of missing commits that were in linux-next that
you're relying on) simply do git rebase --abort.