Upgrade from a direct mode repo to a v7 repo can cause annexed files to get checked into git, in an edge case.

The annexed files need to be already v7 unlocked files, and their content needs to be present in the direct mode repo. Of course this is an unusual situation.

Then, the upgrade to v7 from direct mode makes a commit "commit before upgrade to annex.version 6" which converts the pointer files into the full file content.

Also, git annex sync in the direct mode repo before the upgrade converted the v7 unlocked files back to locked files. (While also a bug, this helped mask the other bug..)

Both fixed now.