I have git repository A that uses B as a submodule.

B's history has been rewritten after an LFS migration, but I would love it if A could still have its entire history functional. After the LFS migration, I do have a mapping OldSHA1 > NewSHA1 for submodule B, and now I just want to rewrite OldSHA1 gitlinks to NewSHA1 in repo A.

I have tried to run a filter-repo command on the repo A with a full OldSHA1==>NewSHA1 mapping as parameter but it doesn't seem to pick up gitlinks.

I also tried filter-branch as detailed in this thread Repository with submodules after rewriting history of submodule that seems to be looking for the exact thing I am trying to accomplish. I tried doing this with a single OldSHA1=>NewSHA1 mapping, and here's the command I am trying to run:

git filter-branch --commit-filter '
  if [ "$GIT_COMMIT" =  ];
  then
    cd ;
    git checkout ;
    cd ..;
    git add -u;
    git commit -m "updated gitlink";
  else
    git commit-tree "$@";
  fi' HEAD 

But I keep getting the following error:

fatal: reference is not a tree: 

Somehow, git checkout doesn't seem to pick up the tree of submodule B. I even tried to specify a path with git -C AbsolutePathToSubModule checkout but I get the same error.

So, a few questions:

• Is there something obvious I'm doing wrong here?
• Is there a better way of accomplishing this? It seems like I "simply" want to replace a string with another somewhere in the object database, but I can't find a simple way to do that
• Is there a way to do this on the entire repo like filter-repo does? Or should I run this on every single branch.

Thanks for any help, advice, clue about how to accomplish this!

Edit 1:

After an answer in the comments, I edited my script to this:

git filter-branch --commit-filter '
  if [ "$GIT_COMMIT" =  ];
  then
    git update-index --add --cacheinfo 160000,,;
  fi
  git commit-tree "$@";
  ' HEAD

But it has no effect :(

WARNING: Ref 'refs/heads/develop' is unchanged

Edit 2:

Thanks a lot to user @torek! This is a snippet to help anyone get started:

git filter-branch --index-filter '
if [ "$(git rev-parse --quiet --verify :)" =  ];
then
  git update-index --cacheinfo 160000,,;
fi' HEAD --all

From then, you have to loop over all OLDSHA1/NEWSHA1 pairs, or use a case) dictionary as depicted in their answer below

Thanks again a lot!