Sometimes when you work on a project long enough, you find that for one reason or the other, parts of the project should be in a separate repository. Either the subdir contains reusable code, to be used on another project, or - as it was in our case today - some part of the project, was needed on many servers, and the rest only on one. We decided to create a separate module to ensure that we did not clone the entire projects for these servers.
There are two steps to this procedure. 1. Get the subdir - with the complete git history into a new repo, and 2. get the new repo in to the old project as a submodule.
This is how you move "Application/scripts/shell" from OldProject into its own repo called NewProject. And then link it as a submodule at the same location it were before.
git clone --no-hardlinks OldProject NewProject
git filter-branch --subdirectory-filter Application/scripts/shell HEAD
git reset --hard
rm -rf .git/refs/original/
git reflog expire --expire=now --all
git gc --aggressive --prune=now
Next you need to set the remote (in our case origin) to the new repo's remote.
git submodule add email@example.com:NewProject.git Application/scripts/shell
-- commit --
git submodule init
git submodule update
-- commit again --
You should now have you former subdirectory as a separate repository, at the same location.