Happens to me too. I did git pull --ff-only on my host, added "include role::visualeditor" to puppet/manifests/site.pp, and tried to run vagrant for the first time in weeks. I tried vagrant up, vagrant reload, and vagrant provision, and all failed early on with variations of the same error as above:

[default] Running provisioner: puppet...
Running Puppet with site.pp...
info: Applying configuration version '1372472629'
notice: /Stage[main]/Role::Visualeditor/Mediawiki::Extension[VisualEditor]/Git::Clone[mediawiki/extensions/VisualEditor]/Exec[git clone mediawiki/extensions/VisualEditor]/returns: fatal: unable to access '/root/.config/git/config': Permission denied

I can vagrant ssh and the wiki is running on http://127.0.0.1:8080/ , but Special:Version says I don't have VisualEditor installed. I'm running Ubuntu 13.04.

Change 71165 had a related patch set uploaded by Ori.livneh:
Set $HOME when git-cloning

https://gerrit.wikimedia.org/r/71165

As of git 1.8.1.1 and above, if the home directory can't be accessed, it results in a fatal error. That was the cause of the error. I fixed it in gerrit change 71165.

[mass-moving from Tools>MediaWiki-Vagrant to separate product. See bug 54041. Filter bugmail on this comment.]