* gnu/packages/python.scm (python-feedgenerator): Update to 1.8.
[arguments]: Remove configure flags.
[inputs]: Move python-setuptools, python-pytz, python-six ...
[native-inputs]: ... to here.
[home-page]: Update project's home-page.

* gnu/packages/python.scm (pelican)[native-inputs]: Remove
python-setuptools.
[propagated-inputs]: Move python-feedgenerator, python-jinja2,
python-pygments, python-docutils, python-pytz, python-blinker,
python-unidecode, python-six, python-dateutil-2 ...
[inputs]: ... to here.

* gnu/packages/python.scm (python2-itsdangerous): Use
'strip-python2-variant'.
[native-inputs]: Add python2-setuptools.
(python-itsdangerous)[inputs]: Remove python-setuptools.
[properties]: Define python2-variant.

* gnu/packages/python.scm (python2-oauthlib): Use 'strip-python2-variant'.
[native-inputs]: Add python2-setuptools.
(python-oauthlib)[inputs]: Remove python-setuptools.
[properties]: Define python2-variant for python2-oauthlib.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.1.

This reverts commit 63655d45, reversing
changes made to 80627f51.

This reverts commit 0118c6ab.

This reverts commit 71a8d3b6.

This reverts commit 63e7796f.

* gnu/packages/gnome.scm (gjs)[arguments]: Skip test_utf8_inout test.

* gnu/packages/gnome.scm (geoclue): Update to 2.4.3.

* gnu/packages/patches/inkscape-drop-wait-for-targets.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/inkscape.scm (inkscape)[source]: Add patch.

* gnu/packages/patches/imlib2-CVE-2016-4024.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/image.scm (imlib2): Use it.

gnu/packages/image.scm (imlib2): Update to 1.4.8.

* gnu/packages/webkit.scm (webkitgtk-2.4): Update to 2.4.11.

* gnu/packages/webkit.scm (webkitgtk): Update to 2.12.1.

* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.22.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.8.

* gnu/packages/linux.scm (linux-libre): Update to 4.5.2.

This follows a convention used by some other GNU packages like Autoconf,
Bison, Coreutils, and Gnulib.

* doc.am: Rename to ...
* doc/local.mk: ... this.
* emacs.am: Rename to ...
* emacs/local.mk: ... this.
* gnu-system.am: Rename to ...
* gnu/local.mk: ... this.
* daemon.am: Rename to ...
* nix/local.mk: ... this.
* Makefile.am: Adapt to them.
* doc/guix.texi (Porting to a New Platform): Adapt documentation.
* guix/config.scm.in (%state-directory, %config-directory): Adapt comments.
* emacs/guix-config.el.in (guix-config-state-directory): Likewise.

* gnu/packages/linux.scm (acpi): New variable.

* guix/scripts/substitute.scm (client-terminal-columns): Sanitize the
client's column number.

* guix/store.scm (set-build-options): Add #:locale parameter and honor
it.
* guix/scripts/substitute.scm (guix-substitute): Install the client's
locale.

* guix/scripts/substitute.scm (assert-valid-narinfo): Use gettext for
messages.

Suggested by Danny Milosavljevic <dannym@scratchpost.org>.

* guix/build/download.scm (nar-uri-abbreviation): New procedure.
* guix/scripts/substitute.scm (process-substitution): Use it instead of
'store-path-abbreviation'.

* guix/build/download.scm (uri-abbreviation): Use 'ellipsis' instead of
"...".  Abbreviate the basename of PATH if needed.

Reported by Roel Janssen <roel@gnu.org>.

* doc/guix.texi (Application Setup)[X.509 Certificates]: New section.
(X.509 Certificates): Add an example of certificates in the profile.

* gnu/packages/openstack.scm (python-mox3): Update to 0.14.0.
[inputs]: Move python-fixtures, python-pbr, python-setuptools,
python-six, python-testtools ...
[native-inputs]: ... to here.

* gnu/packages/openstack.scm (python-stevedore): Update to 1.12.0.
[inputs]: Move python-setuptools, python-docutils, python-mock,
python-oslotest, python-sphinx ...
[native-inputs]: ... to here.

* gnu/packages/maths.scm (armadillo): Update to 6.700.4.

Fixes <http://bugs.gnu.org/23311>.

* guix/build/download.scm (tls-wrap): Add 'set-session-priorities!' call.

* gnu/packages/version-control.scm (git): Update to 2.7.4.
(git-manpages)[source]: Update hash.

* gnu/packages/bittorrent.scm (aria2): Update to 1.22.0.

* gnu/packages/video.scm (mpv): Update to 0.17.0.

* gnu/packages/bioinformatics.scm (htsjdk): Rename to...
(java-htsjdk): ...this.
(ngs-java): Rename to...
(java-ngs): ...this.
(ncbi-vdb)[arguments,inputs]: Use new name.
* gnu/packages/java.scm (swt): Rename to...
(java-swt): ...this.
* gnu/packages/music.scm (tuxguitar)[make-flags,inputs,arguments]: Use
new name of package "swt".

* doc/guix.texi (Java Packages): New subsection.

* gnu/packages/bioinformatics.scm (python2-plastid)[native-inputs]: Move
python2-setuptools from here...
[propagated-inputs]: ...to here.

* gnu/packages/statistics.scm (r): Update to 3.2.5.

* gnu/packages/java.scm (icedtea-8): New variable.