assert(usoa == intermediate) could fail in subsequent filter-repo runs

[louiswpf]

assert(usoa == intermediate) could fail in subsequent filter-repo runs.
This is caused by the metadata stored in $GIT_DIR/filter-repo.

Here is a reproducer:

• test.sh

#!/bin/sh -ex

git init -q repo
cd repo
touch file
git add file
git commit -q -m 'Initial commit'
orig_commit_id="$(git rev-parse HEAD)"
git filter-repo --quiet --to-subdirectory-filter dir0 --force --partial
git reset -q "${orig_commit_id}"
git filter-repo --quiet --to-subdirectory-filter dir1
git filter-repo --quiet --to-subdirectory-filter dir1

$ ./test.sh
+ git init -q repo
+ cd repo
+ touch file
+ git add file
+ git commit -q -m 'Initial commit'
++ git rev-parse HEAD
+ orig_commit_id=3bf1e5885e1dba5a890a91e1e3a3036c9f7fa867
+ git filter-repo --quiet --to-subdirectory-filter dir0 --force --partial
New history written in 0.01 seconds...
Completely finished after 0.02 seconds.
+ git reset -q 3bf1e5885e1dba5a890a91e1e3a3036c9f7fa867
+ git filter-repo --quiet --to-subdirectory-filter dir1
New history written in 0.01 seconds; now repacking/cleaning...
Completely finished after 0.04 seconds.
+ git filter-repo --quiet --to-subdirectory-filter dir1
New history written in 0.01 seconds; now repacking/cleaning...
Traceback (most recent call last):
  File "/usr/bin/git-filter-repo", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/usr/lib/python3.12/site-packages/git_filter_repo.py", line 4973, in main
    filter.run()
  File "/usr/lib/python3.12/site-packages/git_filter_repo.py", line 4936, in run
    self._record_metadata(self.results_tmp_dir(), self._orig_refs)
  File "/usr/lib/python3.12/site-packages/git_filter_repo.py", line 4767, in _record_metadata
    self._compute_metadata(metadata_dir, orig_refs)
  File "/usr/lib/python3.12/site-packages/git_filter_repo.py", line 4712, in _compute_metadata
    assert(usoa == intermediate) # old wasn't pruned => usoa == intermediate
           ^^^^^^^^^^^^^^^^^^^^
AssertionError