Is there a way to stop cluttering up the Pending Changes window with all the .meta files?
In the full client, unfortunately, no. But in the Unity Version Control package within Unity, meta files are displayed with their corresponding asset file.
Hope this helps!
Just curious, I’m wondering why one would want to hide any changes? If a file has changed then I’d want to be told about it in pending changes.
Meta files are not something you have control over, they just clutter up the list making it harder to see what you have actually edited.