[Ubuntu LaunchPad bug #1335391](https://bugs.launchpad.net/ubuntu/+source/etckeeper/+bug/1335391)
(Quoting the LaunchPad bug below, but I have experienced this issue in an identical manner.)

I have configured etckeeper to use git. It works fine if I use apt-get or synaptic packet manager.

But when the update-manger install new packet versions it ends with an "installation failed" message. When I check the status of the git repository in the etc directory, some changes are not commited, e.g.:

    On branch master
    Changes to be committed:
      (use "git reset HEAD <file>..." to unstage)
    
      modified: apt/apt.conf.d/01autoremove-kernels
      modified: init.d/resolvconf

    ProblemType: Bug
    DistroRelease: Ubuntu 14.04
    Package: etckeeper 1.9ubuntu2
    ProcVersionSignature: Ubuntu 3.13.0-29.53-generic 3.13.11.2
    Uname: Linux 3.13.0-29-generic x86_64
    NonfreeKernelModules: wl tbs6982fe tbs6680fe tbs6923fe tbs6985se tbs6928se tbs6982se tbs6991fe tbs6618fe tbs6922fe tbs6928fe tbs6991se
    ApportVersion: 2.14.1-0ubuntu3.2
    Architecture: amd64
    CurrentDesktop: Unity
    Date: Sat Jun 28 09:42:13 2014
    InstallationDate: Installed on 2014-03-30 (89 days ago)
    InstallationMedia: Ubuntu 14.04 LTS "Trusty Tahr" - Daily amd64 (20140329)
    PackageArchitecture: all
    SourcePackage: etckeeper
    UpgradeStatus: No upgrade log present (probably fresh install)
    mtime.conffile..etc.etckeeper.etckeeper.conf: 2014-03-30T16:33:03.109833

> [[done]] --[[Joey]]
