how are "untracked working tree files" even possible in this case?

Hi,

I have a script that runs the following sequence of commands within a clone:

-----
/usr/bin/git rebase --abort (took 148ms)
/usr/bin/git cherry-pick --abort (took 103ms)
/usr/bin/git clean -d -f -x (took 2007ms)
/usr/bin/git reflog expire --expire=now --all (took 106ms)
/usr/bin/git reset --hard --quiet
181def85d58597dfb28729029b2ad76b9fbb09f5 -- (took 60103ms)
/usr/bin/git merge --squash 333def1a1513f84c1eb79e5341ed6ebca0d359a1
(took 1795ms)
Err: '/usr/bin/git merge --squash 333def1a1513f84c1eb79e5341ed6ebca0d359a1'
Exit=128
error: The following untracked working tree files would be overwritten by merge:
.gitignore

[...many more files...]

Please move or remove them before you can merge. Aborting -----

I don't understand how untracked working tree files are possible after "git clean -d -f -x" and "git reset --hard" !

I don't have access to this particular repo, but it's around 30GB when cloned (git directory plus working tree), and around 500,000 files in the working tree when checked out. Note: the "reset --hard" takes 60 seconds here.

- Sylvie