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I use a number of apps where ctrl-d is a common non-destructive shortcut, and can't recall ever encountering one where it was used for delete.

k9s does a delete for ctrl+d

With a prompt, asking for confirmation if I recall correctly...

In ranger, dd is cut/mv and dD is delete, but dD on one file spawns a command with :delete typed in so you have to hit enter to pull the trigger, and doing it with multiple files has the same behavior plus adds a y/N prompt asking if you're sure you want to delete those specific files. This is enough friction to prevent most mishaps, but not enough to be annoying. I would suggest taking inspiration from this.

How do I undo CTRL-d deletes? I almost deleted all my home dir...

I am so sorry to hear about that:(

You can go to "~/.local/share/Trash" all files that you deleted are at there