Why does git filter-branch tree-filter fail to rewrite commit but then leave working directory dirty?

Question

I am attempting to revise a repo (not yet shared, so no worries about breaking anyone else's history) and git filter-branch is behaving in a rather odd fashion.

$ git filter-branch -f --tree-filter /path/to/fixup.sh cross-check
Rewrite ae78489a98f2a9429c559833d8320d5f50a99903 (1/1)Hello? Hello?
Goodbye

WARNING: Ref 'refs/heads/cross-check' is unchanged

The "Hello? Hello?" output is from the script, so I know the script is running.

What's frustrating is that after the command completes, the working directory is then dirty:

$ git status
On branch cross-check
Your branch is up-to-date with 'origin/cross-check'.

Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   .gitattributes
    modified:   tools/lua/lib/lfs.so.1.2.1
    modified:   tools/lua/lib/luadoc/config.lua
    modified:   tools/lua/lib/luadoc/doclet/debug.lua
    modified:   tools/lua/lib/luadoc/doclet/formatter.lua
    modified:   tools/lua/lib/luadoc/doclet/html.lua
    modified:   tools/lua/lib/luadoc/doclet/raw.lua
    modified:   tools/lua/lib/luadoc/init.lua
    modified:   tools/lua/lib/luadoc/lp.lua
    modified:   tools/lua/lib/luadoc/taglet/standard.lua
    modified:   tools/lua/lib/luadoc/taglet/standard/tags.lua

Those are exactly the changes I wanted in the revised commit, but for some reason git isn't able to see them during the git filter-branch operation.

What am I doing wrong here?

(FWIW I've run git filter-branch many, many times before. I'm pretty familiar with it in general, but this one has me stumped.)

Answer 1

(converting comments to answer)

The tree filter is run in a directory that is not the normal working directory for the repository. (The actual directory is derived from from the -d argument to git filter-branch, if you supply one; if you don't supply one, filter-branch starts with .git-rewrite. To this, it looks like the filter-branch script adds /t:

orig_dir=$(pwd)
mkdir -p "$tempdir/t" &&
tempdir="$(cd "$tempdir"; pwd)" &&
cd "$tempdir/t" &&
workdir="$(pwd)" ||
die ""

and then uses files in $tempdir for everything else.)

Thus, if any paths in fixup.sh refer back to the original working directory, git won't see those changes in the temporary trees.