Let\'s see what it is
sub & test
mkdir test sub
cd test && git init && touch R
git add sub
git commit -m "add sub directory"
I want to treat them as one git repo and push them remotely, but now the files under sub directory can not be included ?
They are not included because test sees repo sub as nested git repo, and records only its gitlink, or SHA1, and not its url as it would have if sub had been added as a submodule.
You would need to push sub to a remote url first, and then add it as submodule for test to see sub files.
cd test
git submodule add -- /url/to/sub
Or you would need to use a subtree
cd test
git subtree --prefix sub /url/to/sub master --squash