Sometimes unable to lock the index during pre-commit hook

Hi everyone,

I am the maintainer of https://github.com/Cosium/maven-git-code-format/. maven-git-code-format is a code formatter plugin triggered by git pre-commit hook. On pre-commit, the plugin make use of https://www.eclipse.org/jgit/ to alter the git index to format files.

When performing:
  git add . && git commit -m "Test"
The plugin works without issues

But when performing instead:
  git commit -am "Test"
The plugin fails because it can't lock the index file.

With the commit "all" command, it seems that the index is locked at https://github.com/git/git/blob/master/builtin/commit.c#L419 and kept locked during the pre commit hooks execution.

This difference of behaviour with or without "all" option leaves me puzzled. Are pre-commit hooks expected to be able to manipulate the index? If yes, can we call the current commit "all" behaviour a bug? If no, is there a document specifying what hooks are authorized to do?

Thanks in advance