StGIT: Trouble adding files to non-topmost patch

[Matt McCutchen <matt@mattmccutchen.net>]

I keep a copy of the Eclipse source code checked out from CVS, and I use
StGIT to manage both long-term and short-term local changes to the
source.  (StGIT is so much nicer than shuffling patches by hand!)  My
StGIT patch stack is based on an empty tree; the bottom-most patch
(named "origin") contains the original Eclipse source and the others
contain my changes.  I use "cvs up" to pull updates from Eclipse's
repository, a custom script to load the updates into the git index, and
"stg refresh -p origin" to load them into the patch stack.

However, when the Eclipse developers create new files, I can't seem to
add them to "origin" this way.  After my index-updating script runs,
"git status" shows that the new files have been added to the index,
but "stg refresh -p origin" doesn't change "origin" and the new files
show as untracked again.  Some investigation revealed that the problem
is that, whenever StGIT pops a patch (including as part of "stg refresh
-p"), it resets the index.  Here's the relevant code in git.py:

        def switch(tree_id, keep = False):
            """Switch the tree to the given id
            """
            if keep:
                # only update the index while keeping the local changes
                GRun('read-tree', tree_id).run()

This behavior doesn't affect changes and deletions since StGIT
automatically adds them back to the index, but it completely controverts
additions.  Please provide a direct way to add files to non-topmost
patches.

One could argue that my setup is bad.  I could work around the problem
by loading updates using a separate tree holding a clean CVS checkout,
but then it is less convenient to check out additional modules.  I could
download and import the entire CVS history with git-cvsimport, but that
would take an enormous amount of time and disk space.  I'm open to
practical suggestions for a better setup, but I do hope the problem with
StGIT gets fixed.

[I am off-list; please include me in replies.]

Matt