Clone a subdirectory from github using git

Git isn't geared toward this. Reason being, that whenever you fetch from a repo, your .git/objects folder contains all changes to all files in the repo.*

If you have a choice, I'd separate concerns into Git submodules, which are more-or-less independent git repositories linked together using a parent project (with a .gitmodules file).

Then you can just use symbolic links to make the directory structure you want.

For example:

mkdir parent-project ; cd parent-project
git init
mkdir .my-git-root-folders
git submodule add https://example.com/child.git .my-git-root-folders/child
ln -s .my-git-root-folders/child/path/to/subfolder childmodule
git add childmodule
git commit -m 'Add and link child module'

After this you can access childmodule/some-file as if you were accessing <child repo>/path/to/subfolder/some-file.☥

Git will track symbolic links.‡

Footnotes:

• * Except in cases of shallow clones, which only include the latest revisions for each reachable HEAD. Each file's state is still recorded, however.
• ☥ If your code doesn't specifically test for symbolic links.
• ‡ Windows is known to have problems with symbolic links; you need Administrator access to even create them. For best results, use either Linux, Mac OSX, Windows WSL, or a Linux virtual machine.