gnu: Replace (almost) all uses of /run/setuid-programs.

…those good for master, anyway.

* gnu/packages/admin.scm (ktsuss, opendoas, hosts)
[arguments]: Replace /run/setuid-programs with /run/privileged/bin.
* gnu/packages/containers.scm (slirp4netns)[arguments]: Likewise.
* gnu/packages/debian.scm (pbuilder)[arguments]: Likewise.
* gnu/packages/disk.scm (udevil)[arguments]: Likewise.
* gnu/packages/enlightenment.scm (efl, enlightenment)
[arguments]: Likewise.
* gnu/packages/gnome.scm (gdm, gnome-control-center)
[arguments]: Likewise.
* gnu/packages/linux.scm (singularity)[arguments]: Likewise.
* gnu/packages/lxde.scm (spacefm)[arguments]: Likewise.
* gnu/packages/monitoring.scm (zabbix-agentd)[arguments]: Likewise.
* gnu/packages/virtualization.scm (ganeti)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (xsecurelock)[arguments]: Likewise.
* gnu/services/dbus.scm (dbus-configuration-directory): Likewise.
* gnu/services/ganeti.scm (%default-ganeti-environment-variables):
Likewise.
* gnu/services/monitoring.scm (zabbix-agent-shepherd-service): Likewise.
* gnu/tests/ldap.scm (marionette): Likewise.
* gnu/tests/monitoring.scm (os): Likewise.

system: Use /run/privileged/bin in search paths.

* gnu/system.scm (operating-system-etc-service):
Substitute /run/privileged/bin for deprecated /run/setuid-programs.

services: setuid-program: Populate /run/privileged/bin.

Create /run/setuid-programs compatibility symlinks so that we can
migrate all users (both package and human) piecemeal at our leisure.

Apart from being symlinks, this should be a user-invisible change.

* gnu/build/activation.scm (%privileged-program-directory): New variable.
[activate-setuid-programs]: Put privileged copies in
%PRIVILEGED-PROGRAM-DIRECTORY, with compatibility symlinks to each in
%SETUID-DIRECTORY.
* gnu/services.scm (setuid-program-service-type): Update docstring.
* doc/guix.texi (Setuid Programs): Update @file{} name accordingly.

system: Disallow file-like setuid-programs.

It has been a warning for well over a year now.  Now, with
privileged-programs coming, don't let's support nested deprecation
hacks.

* gnu/system.scm (<operating-system>):
Don't ‘sanitize’ the setuid-programs field.
(ensure-setuid-program-list): Delete syntax.
(%ensure-setuid-program-list): Delete variable.

gnu: kmonad: Update to 0.4.2-1.07cd1cb.

* gnu/packages/haskell-apps.scm (kmonad): Update to 0.4.2-1.07cd1cb.

Change-Id: I8a8d36577804d2221b39b430d26e9fd17204c0de

gnu: r-dmrseq: Update to 1.24.1.

* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.24.1.

Change-Id: I22fb49eee056e0dd5306fec4575fcb38cbe916aa

gnu: r-bgeecall: Update to 1.20.1.

* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.20.1.
[propagated-inputs]: Add r-txdbmaker.

Change-Id: Ia51c1ccdb0e49d8dc74a61f605f00c86718bc1f8

gnu: r-mscoreutils: Update to 1.16.1.

* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.16.1.

Change-Id: I233a01625f223c571dae863c977825d4a2909ee7

gnu: r-scater: Update to 1.32.1.

* gnu/packages/bioconductor.scm (r-scater): Update to 1.32.1.

Change-Id: I0232d463f243505a9b3706d64e6666eb245ceb1c

gnu: r-hdf5array: Update to 1.32.1.

* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.32.1.

Change-Id: Iebab45185f6f1fe3e6919a1e70e45127d9f1124f

gnu: r-s4vectors: Update to 0.42.1.

* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.42.1.

Change-Id: I58dc50344c5eb477da9d4ddd4447bcb41f456037

gnu: r-multiassayexperiment: Update to 1.30.3.

* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.30.3.

Change-Id: Iabbd0c74d7515f8f166827b8b99b2ac49b271c13

gnu: r-universalmotif: Update to 1.22.1.

* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.22.1.

Change-Id: I60a617d120e5da046decb491b7641f1e10aac0cb

gnu: r-clusterprofiler: Update to 4.12.2.

* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.12.2.

Change-Id: I17d837fb314c26fcb26c13240a01c91bc2da9797

gnu: r-enrichplot: Update to 1.24.2.

* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.24.2.

Change-Id: I188e7e908a09337d4bacf4802b1557ddd31048f3

gnu: r-dose: Update to 3.30.2.

* gnu/packages/bioconductor.scm (r-dose): Update to 3.30.2.

Change-Id: Ic07fab82efcbda004d6c7ff21d4ed7b49cc426fb

gnu: r-chippeakanno: Update to 3.38.1.

* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.38.1.

Change-Id: Ia4c89074674f3473e11f3b9e1f9ed828701591f6

gnu: r-qfeatures: Update to 1.14.2.

* gnu/packages/bioconductor.scm (r-qfeatures): Update to 1.14.2.

Change-Id: I93c4fc00d19b18a1e0981f21dd0950d1e1a81f37

gnu: r-seqarray: Update to 1.44.1.

* gnu/packages/bioconductor.scm (r-seqarray): Update to 1.44.1.

Change-Id: I06bb0b45d1a4299e835f7a18c7ed70d847bdb565

gnu: r-msa: Update to 1.36.1.

* gnu/packages/bioconductor.scm (r-msa): Update to 1.36.1.

Change-Id: I91665d8ff4cd7570b5bcad27ff132611a09b8ecc