substitute: Sanitize the client-provided column number.

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

substitute: Install the client's locale.

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

substitute: Internationalize signature and download messages.

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

substitute: Better abbreviate substitute URL in progress report.

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'.

download: 'uri-abbreviation' can abbreviate the URI's basename.

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

doc: Add "X.509 Certificates" section under "Application Setup".

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: python-mox3: Update to 0.14.0.

* 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: python-stevedore: Update to 1.12.0.

* 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: armadillo: Update to 6.700.4.

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

download: Add "%COMPAT" to the priority string.

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

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

gnu: git: Update to 2.7.4 [fixes CVE-2016-2315 and CVE-2016-2324].

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

gnu: aria2: Update to 1.22.0.

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

gnu: mpv: Update to 0.17.0.

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

gnu: Rename Java packages to match new naming specification.

* 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: Add specification for Java packages

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

gnu: python2-plastid: Propagate setuptools.

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

gnu: r: Update to 3.2.5.

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

gnu: Add icedtea-8.

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

doc: Mention 'mkswap' during installation.

Reported by Thierry Micoud <thierrymicoud@gmail.com>.

* doc/guix.texi (Preparing for Installation): Mention 'mkswap'.

gnu: Add python-plastid.

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