First, as an alternative install this version of the Drupal Commerce:
composer create-project --repository=https://raw.githubusercontent.com/drugan/project-base/8.x/packages.json drugan/project-base some-dir --stability dev
If desired, you might not install it as a Drupal site, instead use it as a
repository for all other of your projects (local or remote) to pull from. After
composer installing open .gitignore file in the root of a repo and replace its content
with the following:
hidden.git
PATCHES.txt
web/sites/*/files
web/sites/*/services.yml
web/sites/*/settings.php
web/sites/sites.php
web/sites/settings.local.php
Then in the repo root run this:
touch togglegit.sh && chmod u+x togglegit.sh
Fill the togglegit.sh file with the content as it shown below.
Now, run this:
./togglegit.sh hide
After that as usual:
git add .
git commit -m 'My initial commit'
When you want to update this centralized repo just run this:
./togglegit.sh show
composer update
And after the update:
./togglegit.sh hide
git add .
git commit -m 'Updated and commited'
That way you have all the code of the repo commited as one huge git repository from which you can pull. Or, if you like, just use it as the repository for a particular Drupal Commerce 2.x site.