fatal git errors when updating toolkit

[mosesIRL]

The following is the result of running Maintenance -> Update ToolKit after a clean install on ubuntu 16.04:

AtoMiC ToolKit Updater

This will overwrite any manual changes you made to the script.
Type y/Y and press [ENTER] to continue with update or any other key to exit: y


--->Refreshing packages list...
Hit:1 http://us.archive.ubuntu.com/ubuntu xenial InRelease
Get:2 http://us.archive.ubuntu.com/ubuntu xenial-updates InRelease [102 kB]
Get:3 http://us.archive.ubuntu.com/ubuntu xenial-backports InRelease [102 kB]
Get:4 http://security.ubuntu.com/ubuntu xenial-security InRelease [102 kB]
Ign:5 http://download.opensuse.org/repositories/home:/emby/xUbuntu_16.04  InRele                                                                                        ase
Hit:6 http://download.opensuse.org/repositories/home:/emby/xUbuntu_16.04  Releas                                                                                        e
Fetched 306 kB in 0s (469 kB/s)
Reading package lists... Done

--->Installing prerequisites...
Reading package lists... Done
Building dependency tree
Reading state information... Done
git-core is already the newest version (1:2.7.4-0ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

--->Stashing any local changes...

--->Git stashing any local changes made to ...
fatal: not in a git directory
fatal: not in a git directory
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

--->Updating AtoMiC ToolKit...
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
AtoMiC ToolKit updated successfully.


Press [Enter] key to continue or Ctrl+C to exit...

[TommyE123]

This has now been fixed. You might have to do a manual 'sudo git pull' in the AtoMiC-ToolKit the first time you update to get this fix.