by Matteo Scaramuccia.
Hi Séverin,
you could take a look at MDLSITE-2045 where Eloy is tracking all the changes due to the CSV->GIT migration: MDLSITE-2047 could be the root candidate for your issue.
I'm not really an expert with git to suggest something like git ls-files -m into the new process to trigger e.g. a git checkout -- on each item of the list... better to extract the commit time for each item, something like in http://stackoverflow.com/questions/1964470/whats-the-equivalent-of-use-commit-times-for-git#answer-11543788 and below.
I'll drop these refs into MDLSITE-2047.
HTH,
Matteo