This seems to be a case of a corrupted repo caused by either
a) Upgrading to mavericks and its subsequent upgrade of Xcode b) The Xcode upgrade incurred a few hiccups through its upgrade in itself as my RAM was corrupt and causing hourly kernel panics, just after my mavericks upgrade c) Then, Coda 2 asked to reinstall Xcode command line tools, as it was experiencing a known issue where this was the fix. To cap it all off, I cancelled this download once because I was on a bus and my iPhone internet coverage was poor. d) Definitely my git binary and probably my git version changed throughout this process, and it was a long time since my last commit to that repository.
Definitely a corrupted repository, as confirmed by the reclone and remodification which worked.
In terms of repeatability, I don't think this will come up ever due to the highly idiosyncratic circumstances. I think we can mark this one as an anomalous case, and reaffirm our faith in git.
In git we trust.