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I had thought that git-annex and git submodules couldn't mix. However,
looking at it again, it turned out to be possible to use git-annex quite
sanely in a submodule, with just a little tweaking of how git normally
configures the repository. Details of this still experimental feature are in
[[/submodules]].
There is still some work to be done to make git-annex work with submodules
in repositories on filesystems that don't support symlinks.
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