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If you install gitkraken via snap on Ubuntu you will run into an issue if you try to access a directory outside of the users home directory. This is due to it being built with the new more restrictive permissions.
The simplest solution to this is to remount the directory in question inside your home so that it appears in both places and the snap application can access it.
So assuming you want GitKraken to be able to access the directory /var/www you could create a directory www inside your home directory and remount it accordingly. Then gitkraken could open it from with home
sudo mount -obind /var/www $HOME/www