gnu: diamond: Update to 0.8.17.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.17.

gnu: gnunet-gtk: Configure with gnunet path.

* gnun/packages/gnunet.scm (gnunet-gtk)[arguments]: Add '--with-gnunet'
to #:configure-flags.

Signed-off-by: 宋文武 <iyzsong@gmail.com>

gnu: Add tuxpaint-config.

* gnu/packages/games.scm (tuxpaint-config): New variable.

gnu: Add tuxpaint-stamps.

* gnu/packages/games.scm (tuxpaint-stamps): New variable.

gnu: Add Tux Paint.

* gnu/packages/games.scm (tuxpaint): New variable.
* gnu/packages/patches/tuxpaint-stamps-path.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.

gnu: beets: Update to 1.3.19.

* gnu/packages/music.scm (beets): Update to 1.3.19.
[source]: Remove patch to skip failing tests.
* gnu/packages/patches/beets-image-test-failure.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

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

gnu: python-protobuf: Update to 3.0.0.

* gnu/packages/protobuf.scm (python-protobuf, python2-protobuf):
Update to 3.0.0.

gnu: btrfs-progs: Update to 4.6.1

* gnu/packages/linux.scm (btrfs-progs): Update to 4.6.1.
[native-inputs]: Add WHICH.

gnu: gd: Add fix for gd2_read test.

* gnu/packages/patches/gd-fix-gd2-read-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Add patch.

gnu: protobuf: Update to 2.6.1.

* gnu/packages/protobuf.scm (protobuf): Update to 2.6.1.
[source]: Update to new upstream URL.

size: Fix corner case with multiple items on the command line.

Fixes 'guix size foo bar' when 'foo' is in the local store and 'bar'
isn't, which could lead to an incomplete requisite list.

* guix/scripts/size.scm (requisites*): Partition ITEMS according to
'valid-path?'.  Use 'substitutable-requisites' only on invalid items.

Revert "gnu: gd: Add fix for gd2_read test."

This reverts commit ce290354ec4e97003be5f56042e55b36831818c1.

gnu: gd: Add fix for gd2_read test.

* gnu/packages/patches/gd-fix-gd2-read-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Add patch.

gnu: wireshark: Update to 2.0.5.

* gnu/packages/networking.scm (wireshark): Update to 2.0.5.

gnu: perl-dbd-mysql: Update to 4.035 [fixes CVE-2015-8949].

* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.035.

gnu: linux-libre@4.4: Update to 4.4.16.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.16.

gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207].

* gnu/packages/patches/gd-CVE-2016-5766.patch,
gnu/packages/patches/gd-CVE-2016-6128.patch,
gnu/packages/patches/gd-CVE-2016-6132.patch,
gnu/packages/patches/gd-CVE-2016-6214.patch,
gnu/packages/patches/gd-fix-test-on-i686.patch: Delete files.
* gnu/packages/patches/gd-fix-tests-on-i686.patch: New file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/gd.scm (gd): Update to 2.2.3.
[source]: Update patches field accordingly.

gnu: virt-viewer: Remove SPICE-PROTOCOL from inputs.

This is a followup to ba9e2ee64a566d3bdaa93423a56d1fd613cef5f3.

* gnu/packages/spice.scm (virt-viewer)[inputs]: Remove SPICE-PROTOCOL.

gnu: spice-gtk: Remove LIBUSB from inputs.

This is a followup to 0d05a739d2c78e85bf358c4abdc719ebb3550f5a.

* gnu/packages/spice.scm (spice-gtk)[inputs]: Remove LIBUSB.

gnu: Order module imports in (gnu packages qemu) alphabetically.

* gnu/packages/qemu.scm: Order module imports alphabetically.

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