We are using submodules and we are new to git.
We often see merge conflicts for the submodules themselves, no files are conflicted, just the submodule. There are multiple versions listed in the output of git submodule summary. We resolve them by running git add <submodule> in the superproject.
But today we had a developer lose a commit of the submodule when she resolved the conflict in this manner.
Does running a git add choose the remote version? Shouldn't the contents of the submodule get merged? If she made changes in the submodule and committed them (which I see), then why would that commit disappear after she ran the pull and resolved the conflict?
Both file conflicts and submodule conflicts occur when your current branch and the branch-you-want-to-merge-into have diverged.
It merely means an ambiguous situation exists -- you could legitimately want either to "win" in any given case. So, while it may seem "annoying", they merely highlight your rich options to specify what you want (and you must specify what you want). (And, all that programmers do every day is merely to specify detail.)
It seems like the git-add-the-submodule-on-the-superproject should have worked. However, you also had the option to git-checkout-on-the-superproject right away. This is mentioned in this link (resolving submodule conflicts), which talks about the difference between file conflicts and summodule conflicts, and how to resolve them: