In a few cases it wasn't clear so I left them as-is.
While visiting these moved other things to nativeBuildInputs
when it was clear they were one of these cases:
* makeWrapper
* archive utilities (in order to unpack src)
* a few of these might no longer be needed but leaving for another day
Uses the HTTPS url for cases where the existing URL has a permanent
redirect. For each domain, at least one fixed derivation URL was
downloaded to test the domain is properly serving downloads.
Also fixes jbake source URL, which was broken.