services: hurd-vm: Support persistent images again.

Fixes a regression introduced in bab6434f5855b92631615fdd8a2d2a225da28359
whereby following the example from the manual regarding non-volatile images
would no longer work.

* gnu/services/virtualization.scm (hurd-vm-shepherd-service): Pass ‘image’ to
‘system-image’ only if it’s an image.
* doc/guix.texi (Virtualization Services): Explicitly say that the ‘image’
field can contain a file name.  Remove use of ‘const’ for the ‘image’ field in
persistent image example and adjust text.

Fixes: guix/guix#4130
Reported-by: Maxim Cournoyer <maxim@guixotic.coop>
Change-Id: I1a81ce27fb45978a681310b8a8788ab671b3edf8

image: Create directory indexes for ext4 images.

Fixes a bug whereby the store in ext4 partitions created with
‘guix system image’ would be limited to 65,000 sub-directories.

* gnu/build/image.scm (make-ext-image): Invoke “e2fsck -fDy”.

Fixes: guix/guix#4396
Change-Id: I02d3470fac8bdd8971083be8fce192b72bf6510c

gnu: shepherd-1.0: Update to 1.0.9.

* gnu/packages/admin.scm (shepherd-1.0): Update to 1.0.9.

Change-Id: Ib8b6ecd4ca6658726304a6e573d4f3a5d36d00bb

gnu: pcsc-tools: Update to 1.7.3.

* gnu/packages/security-token.scm (pcsc-tools): Update to 1.7.3.
[arguments]<#:phases>: Remove patch-data-paths.
[native-inputs]: Add autoconf-archive and python-minimal-wrapper; remove
gettext-minimal.

Change-Id: Ifc09fda45ff816aa9f8c9408c101cd708f204bea

gnu: qdigidoc: Update to 4.8.2.

* gnu/packages/security-token.scm (qdigidoc): Update to 4.8.2.

Change-Id: I9c9aad95b89c37790f37a4c4b2c68d8c93463613

gnu: pam-u2f: Update to 1.4.0.

* gnu/packages/security-token.scm (pam-u2f): Update to 1.4.0.

Change-Id: Id9571bcab7284419730f6d27ec82e9d889292fe8

gnu: pam-u2f: Improve style.

* gnu/packages/security-token.scm (pam-u2f)[arguments]: Use
G-Expressions.

Change-Id: Ib9d36b4d22898745ca4ce1ea9dcd8654e452051d

gnu: yubico-piv-tool: Update to 2.7.2.

* gnu/packages/security-token.scm (yubico-piv-tool): Update to 2.7.2.
[inputs]: Add zlib.

Change-Id: I4de36791838ba182445654233a061c1e668f0a95

gnu: yubikey-oath-dmenu: Update to 0.14.0.

* gnu/packages/security-token.scm (yubikey-oath-dmenu): Update to 0.14.0.

Change-Id: I628a3b837953f7a945f9deced927d471d56ba530

gnu: pamtester: Fix build with gcc@14.

* gnu/packages/authentication.scm (pamtester)
[arguments]<#:phases>{force-reconfigure}: New phase.
[native-inputs]: Add autoconf, automake, libtool.

Fixes: guix/guix#4640
Change-Id: I454b6b134a89220a97b0799e2041e459e64efaff
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: xdisorg: Update cliphist to 0.7.0.

* gnu/packages/xdisorg.scm (cliphist): Update to 0.7.0.
[inputs]: Add go-github-com-rivo-uniseg.

Change-Id: I6841fe6be3312b29a0ff152746f4d57f9dd7a6ec
Signed-off-by: Andreas Enge <andreas@enge.fr>

Regenerate CODEOWNERS.

This is a follow-up to commit 0de8d6f51dfeb384f9a3f9cfae2a54bdff16fb09 .

* CODEOWNERS: Check in file changed by "make".

Change-Id: I32cb3c06769a04bb051e5bf865182631f97c02f5

etc: Add rekado to bioinformatics team.

* etc/teams.scm: Make rekado a member of the bioinformatics team.

Change-Id: I0a573882df36b40f1d510664bd086bb461a8e985

etc: Add bioinformatics team.

* etc/teams.scm (bioinformatics): New team.

Change-Id: Ic5d95df8a28e0bb575ef58a0e269b6e82e23cb6a

gnu: python-abjad-ext-rmakers: Replace deprecated input.

* gnu/packages/music.scm (python-abjad-ext-rmakers)[propagated-inputs]:
Remove abjad; add python-abjad.

Change-Id: Id313a44afdfad3643ed9082c97bb3b55041ebec3

gnu: python-abjad-ext-nauert: Replace deprecated input.

* gnu/packages/music.scm (python-abjad-ext-nauert)[propagated-inputs]:
Remove abjad; add python-abjad.

Change-Id: I74b52d2a17126c88e3e8635b4b6a3ff67738d31e

gnu: cgit: Update to 1.2.3-11.76abc40.

* gnu/packages/version-control.scm (cgit): Update to 1.2.3-11.76abc40.
[inputs]: Update git to 2.52.0.

Change-Id: I7bbcaed37288165ba2100fb62487f052a40a5a8b
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: buildah: Update to 1.42.1.

* gnu/packages/containers.scm (buildah): Update to 1.42.1.
[native-inputs]: Replace go-1.23 by go-1.24.

Change-Id: Iedd79d9b2ad05cc0a8a40a314133b292e0c27233

gnu: undbx: Ignore warnings.

* gnu/packages/mail.scm (undbx)[arguments]: Add phase 'disable-Werror.

Change-Id: I2f99bea1de5bb4aea502ffd9b6150f16a8ab46e1

gnu: dsp: Update to 2.0.

* gnu/packages/audio.scm (dsp): Update to 2.0.

Change-Id: Iac512686d2dda1ed9cbcaec042af4c6d021953ad