Thanks. I was modifying php version because when it was last deployed PHP 7 wasn't supported so 5.6 was installed as well so there were two PHP versions on the server.
Feb 10 2017
Jan 13 2017
@aurelijus unfortunately that wasn't it. I had local.json configured.
Jan 9 2017
I'm using a VPS but don't have the facility to easily clone it as is and can't risk it being broken anymore than is now. I will get a small instance setup which reproduces the problem (using ansible to roll out so should be straightforward), that probably won't be until in the week, right now I'm working around it by mirroring and pushing to another remote temporarily.
Jan 8 2017
Oct 15 2016
Sep 24 2016
I can't reproduce it anymore I'm afraid. Before I posted this I tried deactivating the repo, disable/enable the URI to no avail.
After I posted I removed the repo from the command line and recreated it from scratch. It now works. All the details are the same (I'm using a private key).
Works fine now
I've added other repos, observed and hosted (public and private) since posting and they work too. I don't know what caused this to happen on the first repo I created but I can't reproduce it since doing the remove.