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:

backpack-cli/src/database.py

Line 235 in bb2365c

# TODO: items should not be removed, rather 'archived'

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