CLI and docs UX improvements#43
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Improve CLI and documentation clarity around
--advancedpermissions, terminal readability, and key-management UX. Documents thatkeys add/keys updaterequire--advancedto change permissions, incorporates terminal readability improvements from #14 (closes #14), fixessetup --advancedbeing ignored when selecting an existing key, and adds docs link, permission warnings, and restart guidance in the CLI.