gnu: Add guile-colorized.

* gnu/packages/guile.scm (guile-colorized): New variable.

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

activation: Do not create setuid binaries in the store [security fix].

Fixes <https://bugs.gnu.org/28751>.

* gnu/build/activation.scm (activate-setuid-programs)[link-or-copy]: Remove.
Use 'copy-file' instead.

gnu: borg: Update to 1.1.0.

* gnu/packages/backup.scm (borg): Update to 1.1.0.
[native-inputs]: Replace python-sphinx-rtd-theme with
python-guzzle-sphinx-theme.

gnu: Add python-guzzle-sphinx-theme.

* gnu/packages/python.scm (python-guzzle-sphinx-theme,
python2-guzzle-sphinx-theme): New variables.

Co-authored-by: Tobias Geerinckx-Rice <me@tobias.gr>

gnu: kdevelop: Do not hardcode user profile locations in wrapper.

* gnu/packages/kde.scm (kdevelop): [arguments]: Do not add
  ${HOME}/.guix-profile/{share,lib/plugins} to XDG_DATA_DIRS and
  QT_PLUGIN_PATH when wrapping the executable.

tests: databases: Add a simple test for MySQL.

Previously, the activation phase for this service caused some systems using it
to not boot. This test checks that it's possible to boot a system using it,
and at least start the service.

* gnu/tests/databases.scm (%mysql-os, %test-mysql): New variables.
  (run-mysql-test): New procedure.

linux-initrd: Ensure that the guile used in the initrd is referenced.

By referencing guile from the initrd output explicitly, it will be present in
the store when this initrd is used. If the exact guile used within the initrd
isn't present in the store, then after root is switched during the boot
process, loading modules (such as (ice-9 popen)) won't work.

This fixes guix-patches bug #28399, "Fix mysql activation, and add a basic
test".

* gnu/system/linux-initrd.scm (expression->initrd)[builder]: Write out a file
  called references in to the initrd output, which includes the store path for
  guile.

gnu: youtube-dl: Update to 2017.10.07.

* gnu/packages/video.scm (youtube-dl): Update to 2017.10.07.

gnu: offlineimap: Update to 7.1.3.

* gnu/packages/mail.scm (offlineimap): Update to 7.1.3.

services: Remove unneeded imported.

This caused a circular dependency.
Reported by Oleg Pykhalov <go.wigust@gmail.com>
at <https://lists.gnu.org/archive/html/help-guix/2017-10/msg00021.html>.

* gnu/services/networking.scm: Remove unneeded import of (gnu system
base).

gnu: gnome-calendar: Update to 3.26.2.

* gnu/packages/gnome.scm (gnome-calendar): Update to 3.26.2.

gnu: par2cmdline: Update to 0.7.4.

* gnu/packages/backup.scm (par2cmdline): Update to 0.7.4.

gnu: munge: Update to 0.5.13.

* gnu/packages/admin.scm (munge): Update to 0.5.13.

gnu: aisleriot: Update to 3.22.3.

* gnu/packages/gnome.scm (aisleriot): Update to 3.22.3.
[inputs]: Use guile-2.2 instead of guile-2.0.

gnu: Add missing mongodb patch to local.mk.

* gnu/local.mk (dist_patch_DATA): Add the
  mongodb-support-unknown-linux-distributions.patch.

web: Add nginx-documentation.

* gnu/packages/web.scm (nginx): Add comment about updating the documentation.
  (nginx-xslscript): New variable.
  (nginx-documentation): New variable.

perl: Add perl-parse-recdescent.

* gnu/packages/perl.scm (perl-parse-recdescent): New variable.

gnu: Add missing input to python-py3status and fix call path.

file is used to determine configuration file encoding and py3status fails to
start when this tool is missing.

* gnu/packages/python.scm (python-py3status)[inputs]: Add file.
  [arguments]: Modify phases to patch py3status to call file with an absolute
  path.

pull: Add GUIX_PULL_URL environment variable.

* guix/scripts/pull.scm (%repository-url): Add GUIX_PULL_URL environment
  variable.
* doc/guix.texi (Invoking guix pull): Mention GUIX_PULL_URL.

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

gnu: sdl: Add debug output.

* gnu/packages/sdl.scm (sdl, sdl-gfx, sdl-image, sdl-mixer, sdl-net, sdl-ttf):
  Add debug output.

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