Github package does not show file changes until focus out and in again

Description

For my git projects, I created a symlink from /home/user/git to /git. In the last few weeks (or months, I can't exactly remember), I had the following problem: After changing a file and saving it, the tree view highlights the file that has changed, but it is not shown in the unstaged changes area until another app gets the focus and atom gets it back. I created a couple of screenshots to demonstrate this behavior:

After opening a clean git project:

After changing the readme file, the change is highlighted in the project tree but not listed in the unstaged changes area:

After focus out and focus in event, the change is listed:

I first thought #1741 is adressing the same behaviour, but as long as the file is listed in the unstaged changes area, the diffs are shown correctly in the main editor after clicking the file:

Steps to reproduce

Setup a new git project and the github plugin works as expected:

cd /tmp
mkdir test
cd test
git init
touch README.md
git add .
git commit -m "initial commit"
atom .

Also, opening a project without a symlink to a root folder works:

cd /
ln -s /tmp/test /tmp/test2
atom /tmp/test2

But opening a project from the command line with a root symlink (or a nested path, e.g. /test/test), the behaviour is like described above:

cd /
sudo ln -s /tmp/test /test
atom /test

Workaround

Not using symlinks pointing to a root folder

Versions

Ubuntu 18.04 Atom : 1.31.2 Electron: 2.0.7 Chrome : 61.0.3163.100 Node : 8.9.3 Plugins: only plugins of the plain installation