git init
mkdir hoge && mkdir fuga && mkdir source
touch hoge/hoge.txt && touch fuga/fuga.txt && touch source/source.txt
git add . && git commit -am "1st commit"

touch hoge/hoge2.txt     && git add . && git commit -m "2nd commit. add hoge2"
touch fuga/fuga2.txt     && git add . && git commit -m "3rd commit. add fuga2"
touch source/source2.txt && git add . && git commit -m "4th commit. add source2"

mkdir source/folder1/
touch source/folder1/source3.txt
git add .
git commit -m "5th commit. add source/folder1/source3"

git subtree push /c/repos/source/ master --prefix source/