cannot get files to add to git repo

I clone a git repo, then set up a project with repo head folder, when i add a file, it doesn't ask me if i want to add it to repo like in other projects. I have to create the project in folder I cloned to for it to work, but then i don't get npm toolbar. Is it like this on purpose, if i set up the project with the head folder of the repo as the project root i can commit changed files that were already in the repo but i cannot add new ones, it doesn't ask and it won't let me do it manually. It is not set to do it silently.