This is needed for robust handling of the git-annex branch. Since changes
are staged to its index as git-annex runs, and committed at the end,
it's possible that git-annex is interrupted, and leaves a dirty index.
When it next runs, it needs to be able to merge the git-annex branch
as necessary, without losing the existing changes in the index.
Note that this assumes that the git-annex branch is only modified by
git-annex. Any changes to it will be lost when git-annex updates the
branch. I don't see a good, inexpensive way to find changes in
the git-annex branch that arn't in the index, and union merging the
git-annex branch into the index every time would likewise be expensive.
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 <http://git-annex.branchable.com/>
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