There's a number of reasons this could be happening. The main two reasons are that you could've added an ignore pattern that would exclude all files from your root directory showing up for example. This would've been done by going into your repository settings (there's a settings button in the top right of your repository window) and on the advanced tab the top section shows your repository-specific ignore file which you can click 'edit' on to show your ignore patterns.
Alternatively you may have simply changed your view options so it will only show certain files. Make sure it's set to "Show Pending" as the screenshot below shows:
If you could check the above two suggestions first and if neither work we can investigate further.
Hope that helps
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