According to my Eclipse I am working in
$ git status
On branch develop
Your branch is up-to-date with 'origin/develop'.
nothing to commit, working directory clean
If you see files under
git ls-files and they don't show under
git status then probably they are already inside the index, and - most likely - commited.
You can use
git cat-file -p HEAD:filename to check content of object in the repository.
My guess is that you have assume-unchanged (this prevents any changes to show up in status) or skip-worktree flags set inside index. You can check it via
git ls-files -v file. If in first column you see:
git update-index --no-assume-unchanged fileshould help.
syou have skip-worktree flag set as true, and unsetting it should help:
git update-index --no-skip-worktree file
Hit means that file has been commited and it has not been modified.
There's also a possibility that your's index is corrupted, you could try
git update-index --really-refresh or deleting .git/index (Git should recreate that for you when necessary)