Could not create work tree dir 'example.com'.: Permission denied

I think you don't have your permissions set up correctly for /var/www Change the ownership of the folder.

sudo chown -R $USER /var/www

I was facing the same issue but it was not a permission issue.

When you are doing git clone it will create try to create replica of the respository structure.

When its trying to create the folder/directory with same name and path in your local os process is not allowing to do so and hence the error. There was "background" java process running in Task-manager which was accessing the resource of the directory(folder) and hence it was showing as permission denied for git operations. I have killed those process and that solved my problem. Cheers!!

Turns out the problem was in the permission. I fix it with the following command

sudo chown -R $USER /var/www

Please make sure with the $USER variable. I tested and worked on Ubuntu Distro