gnu: libgit2: Fix Clar test framework.

This commit reverts 'patch' hack introduced in
a48a1071a686b250bf8b7982ca0ce8dda1d93c61 and fixes bug in the Clar test
framework.

Patch is proposed to Clar upstream as
<https://github.com/vmg/clar/pull/78>.

* gnu/local.mk: Add libgit2-0.25.1-mtime-0.patch.
* gnu/packages/patches/libgit2-0.25.1-mtime-0.patch: New file.
* gnu/packages/version-control.scm (libgit2)[arguments]:
Remove 'apply-patch' phase.
[inputs]: Remove "patch".
[source]: Add 'patches' field.

Signed-off-by: Sergei Trofimovich <slyfox@inbox.ru>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

daemon: Add '--timeout' and '--max-silent-time'.

* nix/nix-daemon/guix-daemon.cc (GUIX_OPT_TIMEOUT)
(GUIX_OPT_MAX_SILENT_TIME): New macros.
* nix/nix-daemon/guix-daemon.cc (options): Add '--timeout' and
'--max-silent-time'.
(parse_opt): Honor them.
* tests/guix-daemon.sh: Add test.
* doc/guix.texi (Invoking guix-daemon): Document the options.
(Common Build Options): Properly describe default
timeout/max-silent-time value.  Add cross-ref to "Invoking
guix-daemon".

gnu: Add cataclysm-dda.

* gnu/packages/games.scm (cataclysm-dda): New variable.

gnu: allegro: Update to 5.2.2.0.

* gnu/packages/game-development.scm (allegro): Update to 5.2.2.0.

gnu: allegro: Update source uris.

* gnu/packages/game-development.scm (allegro@5.2, allegro@5.0,
allegro@4.4)[source]: Update source uris.

file-systems: Improve error handling in the iso9660 case - fixes boot problem.

* gnu/build/file-systems.scm (read-iso9660-superblock): Modify.

gnu: freeciv: Update to 2.5.7.

* gnu/packages/games.scm (freeciv): Update to 2.5.7.
[source]: Update uri list.

gnu: Remove old vtk module dependence in image-processing.scm.

* gnu/packages/image-processing.scm: Remove old vtk module dependence.

gnu: wine: Update to 2.9

* gnu/packages/wine.scm (wine): Update to 2.9

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: slop: Update to 6.3.41.

* gnu/packages/xdisorg.scm (slop): Update to 6.3.41.

licenses: Add CC-BY 4.0.

* guix/licenses.scm (cc-by4.0): New variable.

gnu: mcelog: Update to 152.

* gnu/packages/linux.scm (mcelog): Update to 152.

gnu: linux-libre@4.1: Update to 4.1.40.

* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.40.

gnu: grub: Run tests sequentially.

Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>
at <http://bugs.gnu.org/26936>.

* gnu/packages/bootloaders.scm (grub)[arguments]: Add #:parallel-tests?.

gnu: sudo: Update to 1.8.20p2.

* gnu/packages/admin.scm (sudo): Update to 1.8.20p2.

gnu: re2: Update to 2017-06-01.

* gnu/packages/regex.scm (re2): Update to 2017-06-01.

.mailmap: Add another alias for ng0.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: neomutt: Update to 20170602.

* gnu/packages/mail.scm (neomutt): Update to 20170602.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>

substitute: Do not display the installed size.

* guix/scripts/substitute.scm (process-substitution): Do not show the
installed size in the "Downloading" message.

ui: 'show-what-to-build' warns when we don't have enough disk space.

* guix/ui.scm (check-available-space): New procedure.
(show-what-to-build): Compute 'installed-size' and call
'check-available-space'.