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If you have no idea what Git is, that warning message is not telling you you’re about to delete 5000 files.
But I wonder if this person maybe does know about Git because they used the word „stage“.
If you don’t know what git is, you should probably avoid choosing the “confirm” option when you’re warned that an operation is dangerous.
That said, I think the change they ultimately made in the linked issue, which words the warning differently and, more importantly, provides an option to only discard changes to already-tracked files, is a vast improvement.
