Following my older recommendation, it boils down to being able to find a repo which actually contains the missing elements (here full trees).
This is what is shown in “How to fix corrupted git repository?”.
But if a full clone doesn’t solve the problem, then it may be:
- a corruption of the repo on the GitHub side (contact GitHub support to check).
- some kind of corruption on the client side (your Ubuntu). Make sure to check if the issue persists with the latest Git release (1.8.5.2-1) from a custom PPA (Personal Package Archive).
Update July 2016, with Git 2.10 soon to be release, you now have:
git fsck --name-objects
See “How to fix git error broken link from tree to tree?” for more.