soft-delete items

[Kaya-Sem]

At this point in time, deleting an item also removes it from every collection it is in. This may not be desirable.
For archival reasons, a solutions needs to be created to soft-remove an item, removing it everywhere except from the collections.

See the code near this line: https://github.com/Kaya-Sem/backpack-cli/blob/bb2365c4c3e09424508e4174527aa400d3ea71bc/src/database.py#L235

Also, look for the number of this issue in the project code base.