This reverts commit f5c6e77a.

* guix/import/gem.scm (guix-package->gem-name,
  gem-package?, latest-release): New procedures.
  (%gem-updater): New variable.
  (rubygems-fetch): Wrap body in
  'call-with-output-file' and 'with-error-to-port'.
* guix/scripts/refresh.scm (%updaters): Add %GEM-UPDATER.
* doc/guix.texi (Invoking guix refresh): Mention RubyGems.

* doc/guix.texi ("invoking guix import"): Add a footnote to the CPAN importer
  on the need for Guile-JSON.

* doc/guix.texi ("build systems"): Drop documentation of
  BUILD-EXPRESSION->DERIVATION.

* doc/guix.texi ("build systems"): Use modify-phases syntax instead of
  alist-delete in example.

* doc/guix.texi ("invoking guix archive"): Move paragraph describing basic
  invocation from the end to the beginning of the section.

* doc/guix.texi: Correct typos, grammar and stylistic points.

Fixes <http://bugs.gnu.org/19816

>.

* guix/scripts/environment.scm (evaluate-input-search-paths)
(build-inputs): Delete.
(evaluate-profile-search-paths, strip-input-name)
(package-or-package+output?, package-environment-inputs)
(build-environment, inputs->profile-derivations): New procedures.
(create-environment, show-search-paths, launch-environment)
(launch-environment/container): Replace 'inputs' argument
with 'profile' argument.
(package+propagated-inputs): Strip off names off of input tuples.
(options/resolve-packages): Handle input tuples that specify an output
in expressions.
(guix-environment): Convert inputs into a profile to use in the
environment.  Remove non-package inputs such as origins from
environment inputs.
* doc/guix.texi ("invoking guix environment"): Document package+output
tuples for --expression option.
* tests/guix-environment.sh: Update tests.
* tests/guix-environment-container.sh: Likewise.

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

* doc/guix.texi (System Installation): Turn all subsections into
individual nodes.
(Limitations): Update the number of packages.
(Preparing for Installation)[Keyboard Layout, Networking, Disk
Partitionning]: New subsections.  Move the 'cow-store' thing to...
(Proceeding with the Installation): ... here.  Describe things in more
detail.
(Base Services): Add index entry for "keyboard layout".

Co-authored-by: Petter <petter@mykolab.ch&gt;.>

Fixes <http://bugs.gnu.org/22572>.
Reported by Mark H Weaver <mhw@netris.org>.

* gnu/system/locale.scm (%not-dot): New variable.
(denormalize-codeset, locale-name->definition): New procedures.
* gnu/system.scm (locale-name->definition*): New procedure.
(operating-system-locale-directory): Instead of raising an error, add
the missing locale.
* doc/guix.texi (Locales): Adjust accordingly.

* doc/emacs.texi (Emacs Commands): Document "M-x guix-edit".
* doc/guix.texi (Invoking guix edit): Mention it.

* doc/guix.texi (operating-system Reference): Mention 'tzselect' and
invalid timezone strings.

Partly fixes <http://bugs.gnu.org/22039>.

* gnu/services/herd.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
* gnu/services/shepherd.scm (shepherd-service-canonical-name): New
procedure.
(shepherd-service-file): Export.
* guix/scripts/system.scm (upgrade-shepherd-services): New procedure.
(switch-to-system): Use it.
* guix/ui.scm (info): New procedure.
* doc/guix.texi (Invoking guix system): Mention system services.

* guix/scripts/build.scm (transform-package-inputs): New procedure.
(%transformations): Add it.
(%transformation-options, show-transformation-options-help): Add
--with-input.
* tests/scripts-build.scm ("options->transformation, with-input"):
("options->transformation, with-input, no matches"): New tests.
* tests/guix-build.sh: Add tests.
* doc/guix.texi (Package Transformation Options): Document it.

* guix/scripts/package.scm (show-help): Call
'show-transformation-options-help'.
(%options): Append %TRANSFORMATION-OPTIONS.
(process-actions)[transform, transform-entry]: New procedures.
* doc/guix.texi (Invoking guix package): Mention package
transformations.
(Package Transformation Options): Mention 'guix package'.

* guix/scripts/build.scm (%transformation-options): New variable.
(show-transformation-options-help): New procedure.
(show-help): Remove '--with-source' documentation and add
'show-transformation-options-help' call.
(%options): Remove "with-source" and append %TRANSFORMATION-OPTIONS.
* doc/guix.texi (Package Transformation Options): New node.  Document
'--with-source', moved from...
(Additional Build Options): ... here.

* doc/guix.texi (Invoking guix build): Add example.  Shuffle options in
the new subsections below.
(Common Build Options, Additional Build Options): New nodes.
(Invoking guix archive): Refer to "Common Build Options".
(Invoking guix environment): Likewise.
(Invoking guix system): Likewise.

fixlet

* doc/images/dmd-graph.dot: Rename to...
* doc/images/shepherd-graph.dot: ... this.
* doc.am (DOT_FILES): Adjust accordingly.
* guix/scripts/system.scm (dmd-service-node-label)
  (dmd-service-node-type, export-dmd-graph): Rename to...
  (shepherd-service-node-label, shepherd-service-node-type)
  (export-shepherd-graph): ... this.
  (show-help, process-action, process-command): Rename 'dmd-graph' to
  'shepherd-graph'.
* emacs/guix-command.el (guix-command-additional-execute-arguments)
  (guix-command-special-executors): Likewise.
* doc/guix.texi: Likewise.
* doc/emacs.texi (Emacs Popup Interface): Likewise.

* gnu/services/shepherd.scm (dmd-root-service-type, %dmd-root-service)
  (dmd-service-type, <dmd-service>, dmd-service, dmd-service?)
  (make-dmd-service, dmd-service-documentation, dmd-service-provision)
  (dmd-service-requirement, dmd-service-respawn, dmd-service-start)
  (dmd-service-stop, dmd-service-auto-start?, dmd-service-modules)
  (dmd-service-imported-modules, dmd-service-file-name, dmd-service-file)
  (dmd-service-back-edges): Rename to...
  (shepherd-root-service-type, %shepherd-root-service, shepherd-service-type)
  (<shepherd-service>, shepherd-service, shepherd-service?)
  (make-shepherd-service, shepherd-service-documentation)
  (shepherd-service-provision, shepherd-service-requirement)
  (shepherd-service-respawn, shepherd-service-start)
  (shepherd-service-stop, shepherd-service-auto-start?)
  (shepherd-service-modules, shepherd-service-imported-modules)
  (shepherd-service-file-name, shepherd-service-file)
  (shepherd-service-back-edges): ...this
* gnu/services.scm: Adjust comments.
* gnu/services/avahi.scm (avahi-dmd-service): Rename to...
  (avahi-shepherd-service): ... this.
* gnu/services/base.scm (%root-file-system-dmd-service)
  (file-system->dmd-service-name, mapped-device->dmd-service-name)
  (dependency->dmd-service-name, file-system-dmd-service)
  (mingetty-dmd-service, nscd-dmd-service, guix-dmd-service)
  (guix-publish-dmd-service, udev-dmd-service, gpm-dmd-service): Rename to...
  (%root-file-system-shepherd-service)
  (file-system->shepherd-service-name, mapped-device->shepherd-service-name)
  (dependency->shepherd-service-name, file-system-shepherd-service)
  (mingetty-shepherd-service, nscd-shepherd-service, guix-shepherd-service)
  (guix-publish-shepherd-service, udev-shepherd-service)
  (gpm-shepherd-service): ... this.
* gnu/services/databases.scm (postgresql-dmd-service): Rename to...
  (postgresql-shepherd-service): ... this.
* gnu/services/desktop.scm (upower-dmd-service, elogind-dmd-service):
  Rename to...
  (upower-shepherd-service, elogind-shepherd-service): ... this.
* gnu/services/dbus.scm (dbus-dmd-service): Rename to...
  (dbus-shepherd-service): ... this.
* gnu/services/lirc.scm (lirc-dmd-service): Rename to...
  (lirc-shepherd-service): ... this.
* gnu/services/mail.scm (dovecot-dmd-service): Rename to...
  (dovecot-shepherd-service): ... this.
* gnu/services/networking.scm (ntp-dmd-service, tor-dmd-service)
  (bitlbee-dmd-service, wicd-dmd-service, network-manager-dmd-service): Rename to...
  (dbus-shepherd-service): ... this.
* gnu/services/ssh.scm (lsh-dmd-service): Rename to...
  (lsh-shepherd-service): ... this.
* gnu/services/web.scm (nginx-dmd-service): Rename to...
  (nginx-shepherd-service): ... this.
* gnu/services/xorg.scm (slim-dmd-service): Rename to...
  (slim-shepherd-service): ... this.
* gnu/system.scm (essential-services): Use '%shepherd-root-service'.
* gnu/system/install.scm (cow-store-service-type): Adjust accordingly.
* guix/scripts/system.scm (dmd-service-node-label, dmd-service-node-type)
  (export-dmd-graph): Likewise.
* tests/guix-system.sh: Likewise.
* tests/services.scm ("dmd-service-back-edges"): Rename to...
  ("shepherd-service-back-edges"): Adjust accordingly.
* doc/guix.texi: Likewise.
* doc/images/service-graph.dot: Use 'shepherd' service name.

* gnu/services/dmd.scm: Rename to...
* gnu/services/shepherd.scm: ... this.
* gnu/system.scm: Use it.
* gnu/system/install.scm: Likewise.
* gnu/services/xorg.scm: Likewise.
* gnu/services/web.scm: Likewise.
* gnu/services/ssh.scm: Likewise.
* gnu/services/networking.scm: Likewise.
* gnu/services/mail.scm: Likewise.
* gnu/services/lirc.scm: Likewise.
* gnu/services/desktop.scm: Likewise.
* gnu/services/dbus.scm: Likewise.
* gnu/services/databases.scm: Likewise.
* gnu/services/base.scm: Likewise.
* gnu/services/avahi.scm: Likewise.
* guix/scripts/system.scm: Likewise.
* tests/services.scm: Likewise.
* tests/guix-system.sh: Likewise.
* doc/guix.texi (Shepherd Services): Adjust accordingly.
* gnu-system.am (GNU_SYSTEM_MODULES): Likewise.
* po/guix/POTFILES.in: Likewise.

* doc/guix.texi: Use 'shepherd'/'herd' instead of 'dmd'/'deco'.  Fix
  info references.

* doc/guix.texi (Application Setup)[Emacs Packages]: New subsection.

* doc/guix.texi (Running GuixSD in a VM): New node.
(Invoking guix system): Add reference to 'Running GuixSD in a VM'.

* emacs/guix-main.scm (%license-param-alist): New variable.
  (license->sexp, find-licenses, license-entries): New procedures.
* emacs/guix-license.el (guix-license-get-entries)
  (guix-license-get-display, guix-license-insert-packages-button)
  (guix-license-insert-comment, guix-license-list-describe)
  (guix-license-list-show-packages): New procedures.
  (guix-licenses): New command.
* doc/emacs.texi (Emacs Licenses): New node.
  (Emacs Interface): Add it.
* doc/guix.texi (Top): Add it.
* NEWS: Mention new interface.

* doc/guix.texi (Version Numbers): Add paragraphs about VCS snapshot
version numbers.

* doc/guix.texi (Networking Services): Remove unneeded backslashes.

This is a followup to e26d5076.

* doc/guix.texi (Initial RAM Disk): #:virtio? defaults to #t.

* doc/guix.texi (Daemon Offload Setup): Fix quoting typo in command.

* doc/guix.texi (Locales): Add missing 's'.

Suggested by David Thompson <dthompson2@worcester.edu>
at <http://bugs.gnu.org/22402>.

* doc/guix.texi (Binary Installation): Explain how to make the Info
manual visible.

Suggested by <swedebugia@riseup.net>.

* doc/guix.texi (Using the Configuration System): Add
@unnumberedsubsubsec.  Explain how to remove services from a list.
Mention (gnu system).

* guix/import/cran.scm (%bioconductor-updater,
latest-bioconductor-release, bioconductor-package?): New procedures.
(cran->guix-package): Support repositories other than CRAN.
(%bioconductor-url, %bioconductor-svn-url): New variables.
(description->package): Update signature to distinguish between packages
from different repositories.
(latest-release): Rename procedure ...
(latest-cran-release): ... to this.
(cran-package?): Do not assume all R packages are available on CRAN.
* tests/cran.scm: Update tests.
* guix/scripts/import/cran.scm: Add "--archive" option and default to
CRAN.
* guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater".
* doc/guix.texi: Document Bioconductor importer and updater.

* guix/scripts/build.scm (show-build-options-help)
(%standard-build-options): Add --keep-going.
* guix/scripts/build.scm (set-build-options-from-command-line): Honor
it.
* doc/guix.texi (Invoking guix build): Document it.

* doc/guix.texi (Build Environment Setup, Substitutes): Document
'http_proxy'.

* doc/guix.texi (Running the Test Suite): Explain 'TESTS'.

* doc/guix.texi (Initial RAM Disk): Document kernel command-line
options.

* doc/guix.texi (Build Systems): Remove extra 's'.

* doc/images/bootstrap-packages.dot: New file.
* doc.am (DOT_FILES): Add it.
* doc/guix.texi (Bootstrapping): Show 'guix graph' commands.  Includes
'images/bootstrap-packages' and comment it.

* doc/guix.texi (Networking Services): Document network-manager-service.

* doc/guix.texi (Invoking guix package): Add elaborate --search example
using recsel and sexes.