gpgme comes with autoconf macros, so needs to be in nativeBuildInputs.
I've removed some redundant inputs as well: we don't need autoconf,
automake and libtool since we have autoreconfHook, and we don't need
gpgme in buildInputs since with --with-gpgme-prefix configure flag
does the same thing.
Set strictDeps to catch regressions.
continuation of #109595
pkgconfig was aliased in 2018, however, it remained in
all-packages.nix due to its wide usage. This cleans
up the remaining references to pkgs.pkgsconfig and
moves the entry to aliases.nix.
python3Packages.pkgconfig remained unchanged because
it's the canonical name of the upstream package
on pypi.
