update-index --index-info producing spurious submodule commits

For reasons too complicated to go into, I have a repository B which has
essentially been cloned from A, and there has been vast amounts of work
on B (thousands of commits, many branches).   These changes have not
been merged back to A.  I want to merge them back, but there's a
directory foo that has changes in B that I can't release.

So, I ran filter-branch with an index filter

  found the merge base with A
  removed foo
  did ls-tree on foo from merge base
    and updated the index

The theory is to make each commit in B look like no changes to anything
under foo, and otherwise the same.

After doing this, Richard noticed that the root tree of commits had a
foo object, but that it was labeled a commit instead of a tree (but in
fact it is a tree).  He noticed because diffs looked like submodules.

I was able to produce a minimal test case, output below, script
attached.  The below output is with 1.7.5.4 on NetBSD/i386 (and /amd64).
1.7.6 (ubuntu/amd64) has the same problem.

So:

  Am I using "git update-index --index-info" wrong?

  Or is there a bug?

Thanks,
Greg

Notice that "cat-file -p HEAD:" shows a tree before, and a commit
afterwards:


+ git init
Initialized empty Git repository in /usr/home/gdt/GIT_TEST/.git/
+ mkdir foo
+ touch foo/bar
+ git add foo
+ git commit -minitial content
[master (root-commit) 6755919] initial content
 0 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 foo/bar
+ git cat-file -p HEAD
tree 72d67e6de0599f72f1265c925316f91f78395787
author Greg Troxel [off-list ref] 1313703545 -0400
committer Greg Troxel [off-list ref] 1313703545 -0400

initial content
+ git cat-file -p HEAD:
040000 tree d87cbcba0e2ede0752bdafc5938da35546803ba5	foo
+ git rm -r foo
rm 'foo/bar'
+ git ls-tree HEAD foo
040000 tree d87cbcba0e2ede0752bdafc5938da35546803ba5	foo
+ git ls-tree HEAD foo
+ git update-index --index-info
+ git diff --staged

diff --git a/foo b/foo
new file mode 160000
index 0000000..d87cbcb
--- /dev/null
+++ b/foo

@@ -0,0 +1 @@
+Subproject commit d87cbcba0e2ede0752bdafc5938da35546803ba5

diff --git a/foo/bar b/foo/bar
deleted file mode 100644
index e69de29..0000000
+ git commit -mmunged foo

[master 3348447] munged foo
 1 files changed, 1 insertions(+), 0 deletions(-)
 create mode 160000 foo
 delete mode 100644 foo/bar
+ git cat-file -p HEAD
tree 04fbd499dbd01afb3241d7f0af8171fde008bfe3
parent 6755919e289665ec46d270672d29b594f992fa03
author Greg Troxel [off-list ref] 1313703545 -0400
committer Greg Troxel [off-list ref] 1313703545 -0400

munged foo
+ git cat-file -p HEAD:
160000 commit d87cbcba0e2ede0752bdafc5938da35546803ba5	foo