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For a single file, you can open the external file in Xcode and cmd + s to save it, it will be refreshed in Xcode. Also, for the quick way you can just chose the external folder in Xcode and cmd + s , it will refresh all your external file in this folder.
The Project navigator displays your project's files and lets you open, add, delete, and rearrange those files. To open the Project navigator, at the top of your project window's navigator area, click the icon that resembles a file folder.
A - Added (This is a new file that has been added to the repository) C - Conflict (There is a conflict in the file) D - Deleted (a file has been deleted) M - Modified (An existing file has been changed)
The down arrow means it is displaying all its contents below. Click it to collapse its contents and it turns to a right arrow.
It's the file untracked by source control.
Those characters refer to the source control.
More reference here
You can add to source control by selecting the untracked files
Following steps resolved issue for me:
Screen
Those are uncommitted files if your using GIT, you need to right click Source Control>Commit Selected File manually. It should take away the "?" on the new version of Xcode 6.3.2 as of today
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