Keep only existing files in git history

gitclean.sh

# this doesn't support renamed/moved files
# from https://stackoverflow.com/a/17909526/801189
# Works fine on Windows with Git bash shell

$ git checkout master
$ git ls-files > keep-these.txt
$ git filter-branch --force --index-filter \
  "git rm  --ignore-unmatch --cached -qr . ; \
  cat $PWD/keep-these.txt | tr '\n' '\0' | xargs -d '\0' git reset -q \$GIT_COMMIT --" \
  --prune-empty --tag-name-filter cat -- --all
  
$ rm -rf .git/refs/original/
$ git reflog expire --expire=now --all
$ git gc --prune=now

# optional extra gc. Slow and may not further-reduce the repo size
$ git gc --aggressive --prune=now