Turns out there was a rather big catch with the setup. Apperently for reason i do not quite understand the user context/profile changed once i called git. This would change the homedir. This can be verified by looking at the Git etc file which does the profile change called: profile:
# Set up USER's home directory
if [ -z "$HOME" -o ! -d "$HOME" ]; then
HOME="$HOMEDRIVE$HOMEPATH"
if [ -z "$HOME" -o ! -d "$HOME" ]; then
HOME="$USERPROFILE"
fi
fi
if [ ! -d "$HOME" ]; then
printf "\n\033[31mERROR: HOME directory '$HOME' doesn't exist!\033[m\n\n"
echo "This is an error which might be related to msysGit issue 108."
echo "You might want to set the environment variable HOME explicitly."
printf "\nFalling back to \033[31m/ ($(cd / && pwd -W))\033[m.\n\n"
HOME=/
fi
# normalize HOME to unix path
HOME="$(cd "$HOME" ; pwd)"
I fixed this issue by forcing the home dir to current user as so:
set HOME=%env.USERPROFILE%
The problem was in an init script of git.
Moreover I had to modifiy the config to:
Host webshop_github
HostName github.com
User git
PreferredAuthentications publickey
IdentityFile ~/.ssh/id_rsa.shop