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Two commands did less, or more, than their names implied.
remove-empty-directories ran find . -type d -empty -delete from whatever the current directory happened to be, so its scope was implicit and easy to misjudge. It now prompts for a root, names that root in the confirmation, and runs find against the shell-quoted root via cj/dwim-shell--empty-dirs-command.
secure-delete ran shred without -u, so it overwrote a file's contents but left the file in place, not the deletion the name and the "permanently destroy" prompt promise. Added -u so it unlinks after overwriting.
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