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Yup, upgrading initrafmstools-live (IIRC that was the package name) throws away the changes made for git-fs. They need to be reapplied and slightly modified to account for upstream changes. I have the commits for this lying around, I'll clean them up and submit a pullreq for this soon.
http://s.natalian.org/2013-06-17/live-boot-initramfs-tools.png
This is on a dev branch btw. Just a note.
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