Thanks all. I'm going to try the simplest method: just run git annex
assistant on both machines, drag the music dir into the annex on both
machines, and let it deal with it. Some unnecessary transferring and
temporary on-disk duplication should not be a problem. I've made a
backup first, just in case.


I think it worked. Git annex assistant did a lot of transferring, and when it was eventually done the number of files and size of the ~/Annex/Music dir is exactly the same on both machines, and the files look fine.

The ~/Annex/.git dirs are quite big though: 640M and 1.5G. I ran git gc --aggressive --prune on them, and got them down to 180M and 894M. That still seems surprisingly large but I guess it's not big enough to cause a problem.
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