Remove file from git repository (history)

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I can’t say for sure without access to your repository data, but I believe there are probably one or more packed refs still referencing old commits from before you ran git filter-branch. This would explain why git fsck --full --unreachable doesn’t call the large blob an unreachable object, even though you’ve expired your reflog and removed the original (unpacked) refs.

Here’s what I’d do (after git filter-branch and git gc have been done):

1) Make sure original refs are gone:

rm -rf .git/refs/original

2) Expire all reflog entries:

git reflog expire --all --expire="0 days"

3) Check for old packed refs

This could potentially be tricky, depending on how many packed refs you have. I don’t know of any Git commands that automate this, so I think you’ll have to do this manually. Make a backup of .git/packed-refs. Now edit .git/packed-refs. Check for old refs (in particular, see if it packed any of the refs from .git/refs/original). If you find any old ones that don’t need to be there, delete them (remove the line for that ref).

After you finish cleaning up the packed-refs file, see if git fsck notices the unreachable objects:

git fsck --full --unreachable

If that worked, and git fsck now reports your large blob as unreachable, you can move on to the next step.

4) Repack your packed archive(s)

git repack -A -d

This will ensure that the unreachable objects get unpacked and stay unpacked.

5) Prune loose (unreachable) objects

git prune

And that should do it. Git really should have a better way to manage packed refs. Maybe there is a better way that I don’t know about. In the absence of a better way, manual editing of the packed-refs file might be the only way to go.

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