After running git-annex get in an unlocked (adjusted) v8 repo with git-annex 8.20200330, I see:

git status will show some files to be modified, since content availability has changed and git-annex was unable to update the index. This is only a cosmetic problem affecting git status; git add, git commit, etc won't be affected. To fix the git status display, you can run: git update-index -q --refresh

And indeed, some of the files I just got show as new, others as modified.

Where can I find more information on what happened here?

How can I run the update-index command safely without listing hundreds of files? Can I just run it over the directories those files were copied to?

Would you consider adding an option to run the update-index automatically where needed?

UPDATE: I just notice that the assistant apparently deleted some files from the git repository. When I check the file path with git log <file> I see the initial addition (locked, on a different machine, not adjusted) and then a deletion of the symlink on the machine where I executed git annex get. This is rather terrifying!

The file is still in the filesystem. The last commit to the annex happened over 30m ago, the last log in daemon.log over 20m ago. The assistant will probably not add these files back? But even if it would. It is dangerous that a simple git annex get leads to delete commits.