gnu: dbus: Update to 1.8.12.

* gnu/packages/glib.scm (dbus): Update to 1.8.12.

gnu: poppler: Update to 0.28.1.

* gnu/packages/pdf.scm (poppler): Update to 0.28.1.  Use the .xz source
  tarball.

gnu: inkscape: Update to 0.48.5.

* gnu/packages/patches/inkscape-stray-comma.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/inkscape.scm (inkscape): Update to 0.48.5.  Remove patch. Use
  the .bz2 source tarball.  Use current libgc.  Add 'fix-test-includes' phase.

gnu: mesa: Update to 10.4.0.

* gnu/packages/gl.scm (mesa): Update to 10.4.0.  Use current libdrm.  Add
  eudev, dri3proto, presentproto, and libxshmfence to inputs.  Add gnu-gettext
  to native-inputs.  Add --enable-xa configure flag.  Add new phases
  'add-missing-m4-files' and 'patch-create_test_cases'.

gnu: libdrm: Update to 2.4.58.

* gnu/packages/xdisorg.scm (libdrm): Update to 2.4.58.

gnu: Add libxshmfence.

* gnu/packages/xorg.scm (libxshmfence): New variable.

services: xorg: Make SLiM sessions configurable.

* gnu/services/xorg.scm (%default-xsessions): New variable.
  (xsessions-directory): New procedure.
  (slim-service): Add #:sessions and #:auto-login-session parameters.
  [slim.cfg]: Honor #:sessions.
  (xinitrc): Adjust accordingly.

Remove 'nix-upstream' submodule.

* nix/sync-with-upstream: Remove.
* bootstrap: Remove uses of 'git submodule' and 'sync-with-usptream'.
* .gitmodules: Remove.

Merge branch 'nix' into 'master'.

gnu: Add bowtie

* gnu/packages/bioinformatics.scm (bowtie): New variable.

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

services: static-networking-service: Switch to (guix build syscalls).

* gnu/services/networking.scm (static-networking-service): Remove
  #:inetutils parameter.  Rewrite using 'configure-network-interface'
  and 'set-network-interface-flags'.

syscalls: Add more procedures for network interfaces.

* guix/build/syscalls.scm (sizeof*, type-size, write-type, write-types,
  read-type, read-types, define-c-struct): New macros.
  (SIOCSIFFLAGS, SIOCGIFADDR, SIOCSIFADDR): New variables.
  (sockaddr-in, sockaddr-in6): New C structs.
  (write-socket-address!, read-socket-address,
  set-network-interface-flags, set-network-interface-address,
  network-interface-address, configure-network-interface): New
  procedures.

gnu: Add Clone.

* gnu/packages/perl.scm (perl-clone): New variable.

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

gnu: cairocffi: Move to python module.

* gnu/packages/gtk.scm, gnu/packages/python.scm (python-cairocffi,
  python2-cairocffi): Move variables from gtk to python module to avoid
  circular dependency.

Reported by Mark H Weaver <mhw@netris.org>

gnu: matplotlib: Add gtk3 backends and optional dependency.  Adjust inputs.

* gnu/packages/python.scm (python-matplotlib, python2-matplotlib): Add gtk3
  backends with the necessary inputs and a 'configure-environment' phase.  Add
  the optional 'python-pillow' dependency.  Move 'python-pyparsing' from
  'inputs' to 'propagated-inputs' as it is required at run time.

gnu: Add cairocffi.

* gnu/packages/gtk.scm (python-cairocffi, python2-cairocffi): New variables.

gnu: Add xcffib

* gnu/packages/python.scm (python-xcffib, python2-xcffib): New variables.

build/python-build-system: Fix easy-install.pth collisions.

* guix/build/python-build-system.scm (rename-pth-file): New rename-pth-file
  phase and corresponding function.

gnu: icecat: Build with PulseAudio support.

* gnu/packages/gnuzilla.scm (icecat)[arguments]: Add
  --enable-pulseaudio.

gnu: linux-libre: Update to 3.18.1

* gnu/packages/linux.scm (linux-libre): Update to version 3.18.1.