If you do not want these files to be added by accident, the first option is adding them to your .gitignore file (details in Pro Git). A simple one of your .gitignore may be:
HEAD description hooks/ info/ sample_app/
Please note that you should add the .gitignore file to your repository if you do not need these files.
The files you mentioned are untracked. as output of your git status command says, theses files are not added to commit. (nothing added to commit but untracked files present (use "git add" to track)
Git uses a track-stage-commit cycle to keep track on your files (details in Pro Git). Files will only be committed to Git repository when they are staged.
As my personal practice, I usually begin with the .gitignore file in GitHub provided ones, then I add some repo specific directories and files to the top of gitignore file with comments, so that I'll get a clear logic of what is ignored in the repository.
# Repo specific settings wiki/ test/ # Object files *.o *.ko # Libraries *.lib *.a *.la *.lo
.git/directory of a Git repository. Did you perhaps do agit initinside a.gitdirectory?