On Mon, May 15, 2017 at 03:13:52PM +0300, Dmitry Monakhov wrote:

Observation #2
It is appeared that git tree was corrupted after crash  :) Defenitely fsync is missed
somewhere in git-core, I've straced it and found 'git clone' does only
two fsync for tmp-pack-xxx files. It seems git's crash consistency is horrably broken.

You'll need to add

[core]
	fsyncobjectfiles = yes

to .gitconfig to make git not play lose with data integrity