Thank you Zenaan for the link. You are right, I am very inexperienced when it comes to git however the command used with the preseed was "git clone https://github.com/project" (d-i preseed/late_command string in-target git clone https://github.com/project). I just forgot to type it in the email :)
The problem is that when ran through preseed, there is no project directory. If I enter the command manually, all good, project folder is created.