Git add all subdirectories
Do,
git add .while in the root of the repository. It will add everything. If you do git add *, it will only add the files * points to. The single dot refers to the directory.
If your directory or file wasn't added to git index/repo after the above command, remember to check if it's marked as ignored by git in .gitignore file.
You can also face problems if a subdirectory itself is a git repository - ie .has a .git directory - check with ls -a.
To remove go to the subdirectory and rm .git -rf.