Currently, git-annex handles merge conflicts of annexed files well. It makes two differently named versions of the conflicting files (A more descriptive naming scheme including date and commit hash would be nice, but that's a different topic).

However, a conflict of git-tracked files is not resolved, leading to merge conflicts being left open after a git annex sync (thus leaving file contents with the weird merge markers <<<<< etc., breaking file contents.)

Could git annex [resolve]merge be extended to also handle those git conflicts and leave the repo in a clean, merged state after git annex sync|pull|assist?

To not confuse users, it could be opt-in (git annex --set annex.resolvegitmerge true), but maybe the default for git annex assist?

On conflict, it would remove the conflicting file and instead create two versions with suffixes either like annexed files or better the commit hash and/or date.

Submodule conflicts can't be resolved like this, in that case I would use the most recent commit of the two in question.

rejected --Joey