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
This solves the `Cannot access native keychain` warning from
IntelliJ-based IDEs. Previously IDEA was unable to find `libsecret` as
it was not part of its library path.
Please keep in mind that the keyring daemon that can be enabled on
NixOS with `services.gnome3.gnome-keyring.enable = true` must be
running.