Partly fixes <https://bugs.gnu.org/44760>.
* guix/build/store-copy.scm (copy-store-item): New procedure.
(populate-store): Use it instead of the inline 'copy-recursively' call.
* guix/scripts/system.scm (copy-item): Likewise.
Pass #:reset-timestamps? and #:deduplicate? to 'register-path'.