The problem

git annex is a bit tricky, and I found that things have improved in later versions of the package, but the latest version available by default for Ubuntu 14.04 is from 2014 when in fact the fixes I needed were in the version from 2015 So, following are instructions on how to install the latest version, enjoy

Prepare for installing

echo "deb data main contrib non-free" | sudo tee /etc/apt/sources.list.d/neurodebian.list
echo "deb trusty main contrib non-free" | sudo tee -a /etc/apt/sources.list.d/neurodebian.list 
sudo apt-key adv --keyserver hkp:// --recv-keys 0xA5D32F012649A5A9
sudo apt update

Verify you are about to install the latest version

apt-cache show git-annex-standalone

You should get:

Package: git-annex-standalone
Source: git-annex
Version: 6.20160307+gitgb095561-1~ndall+1

Note: the version is 6.2016


sudo apt install -y git-annex-standalone