doc: Fix outdated description of the bare-bones example.

Reported by fps on #guix.

* doc/guix.texi (Using the Configuration System): Replace mention of
  Emacs with tcpdump.

services: Add 'linux-bare-metal-service-type'.

* gnu/services.scm (modprobe-wrapper): Remove.
  (activation-script): Do not use it.  Remove calls to
  'activate-modprobe' and 'activate-ptrace-attach' in gexp.
  (%modprobe-wrapper, %linux-kernel-activation,
  linux-bare-metal-service-type, %linux-bare-metal-service): New
  variables.
* gnu/system.scm (essential-services): Add %LINUX-BARE-METAL-SERVICE to
  the list, unless CONTAINER? is true.

gnu: ffmpeg: Move flags into their own argument.

* gnu/packages/video.scm (ffmpeg)[arguments]: Move the configurable
  configure flag literals into the configure-flags argument. Call
  configure with these flags from the configure phase.

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

scripts: environment: Allow mixing regular and ad-hoc packages.

This patch changes the --ad-hoc flag to be positional.  That is, the
packages that appear before --ad-hoc are interpreted as packages whose
inputs should be in the environment; the packages that appear after are
interpreted as packages to be directly added to the environment.

* guix/scripts/environment.scm (tag-package-arg, compact): New
  procedures.
  (%options): Tweak the handlers for --load and --expression options.
  (options/resolve-packages): Preserve package mode tag.
  (parse-args): Tweak argument handler to use package tagging procedure.
  (guix-environment): Apply ad-hoc behavior on a per package basis.
* tests/guix-environment.sh: Add test.
* doc/guix.texi ("invoking guix environment"): Document new behavior of
  --ad-hoc.

services: Add screen-locker service.

* gnu/system/linux.scm (base-pam-services): Remove "xlock" and
  "xscreensaver".
* gnu/services/xorg.scm (<screen-locker>): New record type.
  (screen-locker-pam-services, screen-locker-setuid-programs,
  screen-locker-service): New procedures.
  (screen-locker-service-type): New variable.
* gnu/services/desktop.scm (%desktop-services): Use them.
* doc/guix.texi (X Window): Document 'screen-locker-service'.
  (Desktop Services): Mention it.

system: File systems depend on their corresponding device mappings.

Fixes a regression introduced in commit 0adfe95.

* gnu/system.scm (other-file-system-services)[requirements]: Remove.
  [add-dependencies]: New procedure.
  Use it.
* gnu/system/file-systems.scm (<file-system>)[dependencies]: Update
  comment.
* gnu/services/base.scm (mapped-device->dmd-service-name,
  dependency->dmd-service-name): New procedures.
  (file-system-service-type): Use it.

gnu: Add libchop.

* gnu/packages/backup.scm (libchop): New variable.

gnu: Move gdbm to (gnu packages databases).

* gnu/packages/gdbm.scm: Remove.
* gnu/packages/databases.scm (gdbm): New variable, from gdbm.scm.
* gnu/packages/avahi.scm, gnu/packages/cyrus-sasl.scm,
  gnu/packages/guile.scm, gnu/packages/mail.scm,
  gnu/packages/man.scm, gnu/packages/pulseaudio.scm,
  gnu/packages/python.scm, gnu/packages/ruby.scm,
  gnu/packages/sawfish.scm: Adjust accordingly.
* gnu-system.am (GNU_SYSTEM_MODULES): Remove gdbm.scm.

doc: Mention Nix in the intro.

* doc/guix.texi (Introduction): Mention Nix with a xref to
  "Acknowledgments".
  (Acknowledgments): Add link to nixos.org.

system: grub: Let GRUB choose the best graphics mode.

On PCs, it means that it will typically choose resolutions higher
than 640x480, which is nicer.

* gnu/system/grub.scm (eye-candy)[setup-gfxterm-body]: Leave 'gfxmode'
  unset.

gnu: openblas: Update to 0.2.15.

* gnu/packages/maths.scm (openblas): Update to 0.2.15.

gnu: icedtea7: Update to 2.6.2.

* gnu/packages/java.scm (icedtea7): Update to 2.6.2.

gnu: ghc-glut: Propagate freeglut input.

* gnu/packages/haskell.scm (ghc-glut): Move freeglut to
  propagated-inputs.

gnu: bluez: Update to 5.35.

* gnu/packages/linux.scm (bluez): Update to 5.35.

gnu: magit-svn: Update to 2.1.1.

* gnu/packages/emacs.scm (magit-svn): Update to 2.1.1.

gnu: magit: Update to 2.3.0.

* gnu/packages/emacs.scm (magit): Update to 2.3.0.

services: Add 'modify-services'.

* gnu/services.scm (%modify-service, modify-services): New macros.
* gnu/services/base.scm (mingetty-service-type, guix-service-type):
  Export.
* emacs/guix-devel.el (guix-devel-keywords): Add 'modify-services'.
  Ditto in 'guix-devel-scheme-indent' call.
* doc/guix.texi (Using the Configuration System): Give an example of
  'modify-services'.
  (Service Reference): Document it.

services: 'guix-configuration' has a 'substitute-urls' field.

* gnu/services/base.scm (<guix-configuration>)[substitute-urls]: New
  field.
  (guix-dmd-service): Honor it.
* doc/guix.texi (Base Services): Document it.

refresh: Support comma-separated updater types.

* guix/scripts/refresh.scm (%options): Handle comma-separated types for
  '--type' option.
  (guix-refresh): Adjust accordingly.
  (show-help): Likewise.
* doc/guix.texi (Invoking guix refresh): Document it.

gnu: pbtranscript-tofu: Update to 2.2.3.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3.
  [source]: Remove bundled Cython sources in a snippet.  Replace
  ".tar.gz" extension in file-name field with "-checkout".
  [arguments]: Replace "enter-directory-and-clean-up" phase with
  "enter-directory" phase, and add "patch-setuppy" phase.
  [inputs]: Add python2-h5py.  Move python2-cython ...
  [native-inputs]: ... to this field.