gnu: Purge pre-1.3.0 deprecated packages.

* gnu/packages/bioinformatics.scm (deeptools): Remove variable.
* gnu/packages/efi.scm (efi_analyzer): Ditto.
* gnu/packages/guile.scm (guile-2.2/bug-fix, guile-json): Ditto.
* gnu/packages/image.scm (libjpeg): Ditto.
* gnu/packages/kde.scm (kdevplatform): Ditto
* gnu/packages/linphone.scm (linphoneqt): Ditto.
* gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): Ditto.
* gnu/packages/mpi.scm (hwloc-2.0): Ditto.
* gnu/packages/music.scm (python-abjad, zlfo): Ditto.
* gnu/packages/perl.scm (perl-base, perl-parent): Ditto.
* gnu/packages/tryton.scm (python-trytond): Ditto.
* gnu/packages/video.scm (gnome-mpv): Ditto.
* tests/graph.scm: Use guile-json-1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add bpftool.

* gnu/packages/linux.scm (bpftool): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

gnu: erlang: Update to 25.3.

* gnu/packages/lisp.scm (erlang): Update to 25.3.
[native-inputs]: Update erlang-manpages to 0vnpds5.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

po: Do not auto-translate cross-references to other manuals.

Reported by Gottfried at
<https://lists.gnu.org/archive/html/help-guix/2023-04/msg00000.html>.

* guix/build/po.scm (xref-regexp): Dispatch on the number of
arguments.  Ensure there is no info-manual argument or it is empty.
(translate-cross-references): Adapt to changed regexp.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: hwloc: Update to 2.9.1.

* gnu/packages/mpi.scm (hwloc-2): Update to 2.9.1.

Patch to skip tests requiring /sys on non-x86 systems should not be
necessary anymore, as https://github.com/open-mpi/hwloc/pull/570 has
been merged in this new version.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

news: Add entry for the linux-libre-lts 6.1 update.

* etc/news.scm: Add entry.

gnu: linux-libre-lts: Update to 6.1.

6.1 is the newest long-term support version of the kernel.

* gnu/packages/linux.scm (linux-libre-lts-version, linux-libre-lts-gnu-revision,
linux-libre-lts-pristine-source, linux-libre-lts-source, linux-libre-lts): Use
linux-libre-6.1.

Signed-off-by: Jonathan Brielmaier <jonathan.brielmaier@web.de>

news: Add 'de' translation.

* etc/news.scm: Add German translation of 'guix shell -CW' entry.

home: xdg-base-directories: Set correct value for XDG_STATE_HOME.

XDG Base Directory Specification 0.8 officially introduces the
XDG_STATE_HOME environment variable.

Fixes <https://issues.guix.gnu.org/issue/61809>.

* gnu/home/services/xdg.scm
(home-xdg-base-directories-configuration)[state-home]: Set default value
according to spec.  Update field documentation.
(home-xdg-base-directories-service-type): Update service description.

Signed-off-by: Andrew Tropin <andrew@trop.in>

gnu: linux-libre 6.1: Update to 6.1.23.

* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.23.
(linux-libre-6.1-pristine-source): Update hash.

gnu: linux-libre: Update to 6.2.10.

* gnu/packages/linux.scm (linux-libre-6.2-version): Update to 6.2.10.
(linux-libre-6.2-pristine-source): Update hash.

news: Add entry for 'guix shell --container --nesting'.

* etc/news.scm: Add entry.

environment: Add '--nesting'.

* guix/scripts/environment.scm (show-environment-options-help)
(%options): Add '--nesting'.
(options/resolve-packages): Handle it.
(launch-environment/container): Add #:nesting? and honor it.
[nesting-mappings]: New procedure.
(guix-environment*): Add support for '--nesting'.
* guix/scripts/shell.scm (profile-cached-gc-root): Special-case
'nesting?'.
* tests/guix-environment-container.sh: Test it.
* doc/guix.texi (Invoking guix shell): Document it.

gnu: rizin: Update to 0.5.2.

* gnu/packages/engineering.scm (rizin): Update to 0.5.2.
[arguments]: Remove libuv. Add lzma, libmspack and swift_demangler. Skip the analysis_var test.
[inputs]: Add libmspack.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: janet: Update to 1.27.0.

* gnu/packages/lisp.scm (janet): Update to 1.27.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: libexif: Update to 0.6.24. [fixes CVE-2020-0198, CVE-2020-0452]

* gnu/packages/photo.scm (libexif): Update to 0.6.24.
[source]: Switch to git checkout.
[native-inputs]: Add autoconf, automake, gettext-minimal and libtool.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: tcsh: Fix riscv64 cross-compilation.

* gnu/packages/shells.scm (tcsh): fix riscv64 cross-build.
[arguments]<#:phase>: Add 'update-config-scripts' phase for riscv64.
[native-inputs]: Add CONFIG for riscv64.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add avfs.

* gnu/packages/file-systems.scm (avfs): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: pounce: Update to 3.1.

* gnu/packages/messaging.scm (pounce): Update to 3.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: r-ranger: Update to 0.15.1.

* gnu/packages/statistics.scm (r-ranger): Update to 0.15.1.