Almost empty git repo has huge size

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I had an iOS repo on bitbucket and reached a limit of 4Gb. The repo started to deny any commits.

I decided to remove Pods folder using one of these instructions:

Remove folder and its contents from git/GitHub's history

https://stellarflavor.com/2021/12/25/how-to-remove-pushed-pods-folder-from-git-repository/

The repo denied "force push" even if it reduces the repo size so I decided to drop all existing commits to the initial one which contains one small file (.gitignore).

The problem is I reduced repo size to acceptable limit but the .git folder is still huge (more than 99% of whole repo size even when git history is fully dropped). Why does it happen and how to fix it?

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