Following up on clarify that v7 applies to all clones, the next step was to fetch all content from the central, still v5 repository, which worked fine.

But weirdly, some files showed up as modified:

$ git annex get
$ git status
## master...origin/master
 M calendrier/photos/DSCF0879.jpg
 M calendrier/photos/DSCF1191.jpg

Strangely, git doesn't see which changes are present here:

$ git diff
[... takes some time, but no output ...]

Workaround: git checkout . - but I don't understand why that is happening in the first place... Is that a bug? -- anarcat

update: yes, and it was fixed by joeyh.