I started work on a new project and found I had the following when I launched Xcode:
Changes not staged for commit:
modified: <project>.xccheckout
and
Untracked files: 
<project>/xcshareddata/
I then edited .gitignore to ignore .xccheckout and checked the status. It now read as follows:
Changes not staged for commit:
modified: .gitignore
modified: <project>.xccheckout
i.e. the Untracked files mentioned previously were no longer being output by git. I've tried this several times and it's completely reproducible - but completely inexplicable.
 
    