I had a similar situation. I deleted a git, recreated it, refreshed it. All the files showed in Unstaged Changes. Plus and Double Plus did not appear to move them into Staged Changes.

So I Restarted Eclipse and then when I clicked inside an open editor for one of the files, suddenly the files all appeared in Staged Changes. That is because of the Link with Editor state being enabled. I was able to change files and move from Unstaged to Staged as usual. I was able to make the first commit at that point with no issues.

It seemed necessary to Restart to update the view, which seemed not to update otherwise. After that, clicking the Repository in the Git Repositories tab (View) would probably have revealed the same as clicking in an editor.

Eclipse 2025-09 (4.37.0) Build id: 20250905-1456.