gnu: packages: Remove last year's deprecations.

* gnu/packages/admin.scm (guile3.0-shepherd): Remove variable.
* gnu/packages/benchmark.scm (imb-openmpi): Likewise.
* gnu/packages/boost.scm (boost-with-python3): Likewise.
* gnu/packages/pep.scm (python-pep-adapter)[inputs]: Adjust accordingly.
* gnu/packages/cpp.scm (nlohmann-json-cpp): Likewise.
* gnu/packages/games.scm (openrct2)[inputs]: Adjust accordingly.
* gnu/packages/cups.scm (escpr): Likewise.
* gnu/packages/django.scm (python-django-jsonfield): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-modus-operandi-theme)
(emacs-modus-vivendi-theme): Likewise.
* gnu/packages/engineering.scm (kicad-i18l): Likewise.
* gnu/packages/enlightenment.scm (enlightenment-wayland): Likewise.
* gnu/packages/firmware.scm (opensbi-qemu-virt, opensbi-qemu-sifive-u):
Likewise.
* gnu/packages/fonts.scm (font-gnu-freefont-ttf, font-open-dyslexic):
Likewise.
* gnu/packages/game-development.scm (guile3.0-chickadee)
(python-sge-pygame): Likewise.
* gnu/packages/games.scm (retux)[inputs]: Adjust accordingly.
* gnu/packages/gnome-xyz.scm (numix-theme): Likewise.
* gnu/packages/gnupg.scm (guile3.0-gcrypt): Likewise.
* gnu/packages/gstreamer.scm (gst-transcoder): Likewise.
* gnu/packages/gtk.scm (guile3.0-cairo, guile3.0-present, guile3.0-rsvg):
Likewise.
* gnu/packages/guile-xyz.scm (guile3.0-colorized, guile3.0-commonmark)
(guile3.0-config, guile3.0-email, guile3.0-fibers, guile3.0-gi)
(guile3.0-hall, guile3.0-hashing, guile3.0-haunt, guile3.0-ics)
(guile3.0-irregex, guile3.0-lib, guile3.0-mcron, guile3.0-minikanren)
(guile3.0-ncurses, guile3.0-ncurses/gpm, guile3.0-newt, guile3.0-parted)
(guile3.0-pfds, guile3.0-picture-language, guile3.0-semver)
(guile3.0-simple-zmq, guile3.0-squee, guile3.0-syntax-highlight)
(guile3.0-websocket, guile3.0-wisp, guile3.0-xapian): Likewise.
* gnu/packages/guile.scm (define-deprecated-guile3.0-package)
(guile3.0-json, guile3.0-gdbm-ffi, guile3.0-sqlite3)
(guile3.0-bytestructures, guile3.0-git): Likewise.
* gnu/packages/haskell-apps.scm (ghc-stylish-haskell): Likewise.
* gnu/packages/linux.scm (linux-libre-arm-veyron): Likewise.
* gnu/packages/mail.scm (guile3.0-mailutils): Likewise.
* gnu/packages/monitoring.scm (python2-graphite-web): Likewise.
* gnu/packages/package-management.scm (guile3.0-guix): Likewise.
* gnu/packages/package-management.scm (python-conda): Likewise.
* gnu/packages/phabricator.scm (libphutil): Likewise.
* gnu/packages/plotutils.scm (guile3.0-charting): Likewise.
* gnu/packages/python-xyz.scm (python2-smmap2, python-glances)
(python-smmap2): Likewise.
* gnu/packages/shells.scm (oil-shell): Likewise.
* gnu/packages/sqlite.scm (sqlite-with-column-metadata): Likewise.
* gnu/packages/ssh.scm (guile3.0-ssh): Likewise.
* gnu/packages/terminals.scm (et): Likewise.
* gnu/packages/tls.scm (guile3.0-gnutls): Likewise.
* gnu/packages/vlang.scm (v): Likewise.
* gnu/packages/vpn.scm (wireguard): Likewise.
* gnu/packages/web-browsers.scm (next, sbcl-next): Likewise.
* gnu/packages/xorg.scm (transset-df): Likewise.

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