I doubt that warning has ever been right, but I'm sure it is not right
now.
For there to be a risk of git gc deleting objects that are in the annex
index, journal files would have to be staged into it, and deleted, but
the index not committed to the git-annex branch. And AFAICS, there is no
code path where that actually happens. I considered adding one recently,
but didn't.
The way it actually works is, as long as the user has annex.alwayscommit=false
the data lives in the journal, where it's safe from git gc. Then when
git-annex is run w/o that config, the journal is staged into the index,
which is immediately committed to the branch. There's no window where
git gc could delete the objects, because git gc only deletes objects
after some time (2 weeks by default).
Now, if git-annex gets suspended at just the wrong time, or interrupted,
then yes, it's possible. But doesn't matter whether that config was ever
set or not. And many uses of git-annex also recover from that situation
by committing to the git-annex branch.
git-annex allows managing files with git, without checking the file
contents into git. While that may seem paradoxical, it is useful when
dealing with files larger than git can currently easily handle, whether due
to limitations in memory, checksumming time, or disk space.
For documentation, see doc/ or <https://git-annex.branchable.com/>
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