you can see what is not committed or staged yet with
git status
This should show that those files are not tracked yet. You can start to track them by adding them to the index:
git add .project
or add all files (not recommended if you don't have a proper .gitignore defined yet):
git add .
or
git add -A
if you want to stage deletions as well.
The other thing that could be happening here is that you are simply not seeing that the .project file is there. OSes usually hide these by default. Use
ls -A
to include these types of files in the directory listing. To see the contents of what git stored in the last commit, you can also use
git ls-tree HEAD