gnu: Add spice-vdagent.

* gnu/packages/spice.scm (spice-vdagent): New variable.

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

gnu: Add spice.

* gnu/packages/spice.scm (spice): New variable.

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

gnu: Add spice-gtk.

* gnu/packages/spice.scm (spice-gtk): New variable.

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

gnu: Add spice-protocol.

* gnu/packages/spice.scm (spice-protocol): New variable.

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

gnu: Add virglrenderer.

* gnu/packages/spice.scm (virglrenderer): New variable.

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

gnu: Add usbredir.

* gnu/packages/spice.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

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

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

This reverts commit ae46cd0e4cfb1f06d099b2cda1f9e702e86c90e9.

guix package: Suggest prefix search path settings.

* guix/scripts/package.scm (build-and-use-profile): Pass #:kind 'prefix
to 'display-search-paths'.

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: commencement: 'guile-final' is now "hidden".

This way, we no longer have this annoying warning:

  $ guix build guile -n
  guix build: warning: ambiguous package specification `guile'
  guix build: warning: choosing guile-2.0.11 from gnu/packages/guile.scm:128:2

* gnu/packages/commencement.scm (guile-final): Use 'hidden-package'.
* tests/packages.scm ("fold-packages, hidden package"): New test.

packages: Add 'hidden-package'.

* guix/packages.scm (hidden-package, hidden-package?): New procedures.
* gnu/packages.scm (fold-packages): Filter out 'hidden-package?'.
* tests/packages.scm ("hidden-package"): New test.

gnu: Add asciinema.

* gnu/packages/terminals.scm (asciinema): New variable.

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

gnu: gnome: Propagate file-roller.

* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add file-roller.

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

doc: Discourage software bundling.

Fixes <http://bugs.gnu.org/24008>.
Suggested by ng0 <ng0@we.make.ritual.n0.is>.

* doc/contributing.texi (Submitting Patches): Add item about bundling.

doc: Send changes in your patch which are related.

* doc/contributing.texi (Submitting Patches): New @item:
This gives information about sending related changes and examples on
what we view as related changes.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

doc: Mention separate branch for packages with many dependents.

Suggested by ng0 <ng0@we.make.ritual.n0.is>.

* doc/contributing.texi (Submitting Patches): Add note on packages with
more than 100 dependents.

gnu: r-genomicfeatures: Update to 1.24.5.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.

gnu: r-bsgenome: Update to 1.40.1.

* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.

gnu: r-iranges: Update to 2.6.1.

* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.

gnu: r-limma: Update to 3.28.17.

* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.