* gnu/packages/bioinformatics.scm (bio-locus): New variable.

This reverts commit b429c4fb.

* gnu/packages/bioinformatics.scm (bio-locus): New variable.

* gnu/system/linux-container.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
* gnu/system.scm: Export 'operating-system-etc-directory',
  'operating-system-boot-script', 'operating-system-locale-directory', and
  'file-union'.
  (operating-system-boot-script): Add #:container? keyword argument.
  (operating-system-activation-script): Add #:container?  keyword argument.
  Don't call 'activate-firmware' or 'activate-ptrace-attach' when activating a
  container.

Previously, the Ruby build system only knew how to work with gem archives,
which made it difficult to build unreleased gems from a Git repository or
released gems in tarball form.

* gnu/build/ruby-build-system.scm (gnu:unpack, gem-archive?): New procedures.
  (unpack): Use GNU build system unpack phase for non-gem sources.
  (build): Rebuild the gemspec iff the source is a gem archive.
* guix.texi ("ruby-build-system"): Mention that tarballs and directories are
  acceptable.

* gnu/packages/openstack.scm (python-oslo.utils, python2-oslo.utils): New variables.

* gnu/packages/openstack.scm (python-debtcollector,
  python2-debtcollector): New variables.

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

* gnu/packages/python.scm (python-iso8601, python2-iso8601): New variables.

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

* gnu/packages/openstack.scm (python-oslo.config, python2-oslo.config): New variables.

* gnu/packages/openstack.scm (python-stevedore, python2-stevedore): New variables.

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

* gnu/packages/version-control.scm (cvs-fast-export): New variable.

* gnu/packages/gnupg.scm (gnupg): Update to 2.1.8.

* gnu/packages/cpio.scm (cpio): Update to 2.12.
  [source]: Remove 'patches' field.
* gnu/packages/patches/cpio-CVE-2014-9112-pt1.patch,
  gnu/packages/patches/cpio-CVE-2014-9112-pt2.patch,
  gnu/packages/patches/cpio-CVE-2014-9112-pt3.patch,
  gnu/packages/patches/cpio-CVE-2014-9112-pt4.patch,
  gnu/packages/patches/cpio-CVE-2014-9112-pt5.patch,
  gnu/packages/patches/cpio-fix-symlink-bad-length-test.patch: Remove.
* gnu-system.am (dist_patch_DATA): Remove.

* gnu/packages/game-development.scm (tiled): Update to 0.13.1.

* gnu/packages/databases.scm (redis): Update to 3.0.4.

This reverts commit daa48c31.

* gnu/packages/compression.scm (lz4): New variable.

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

* gnu/services/base.scm (mingetty-service): Change default value of
  #:motd from a monadic value to a <plain-file>.  Assume MOTD to be a
  file-like object.  Assume LOGIN-PROGRAM is a gexp or #f.
  (%base-services): Use 'plain-file' instead of 'text-file' for motd.
* gnu/system/linux.scm (unix-pam-service): Update docstring to mention
  that MOTD is a file-like object.
* doc/guix.texi (Base Services): Adjust 'mingetty-service' documentation
  accordingly.

* gnu/packages/ibus.scm (ibus-libpinyin): New variable.

* gnu/packages/ibus.scm (libpinyin): New variable.

* gnu/packages/games.scm (minetest-data, minetest): Update to 0.4.13.

This reverts commit 5cfb91c7.

* gnu/packages/compression.scm (lzo): Update to 2.09.

* gnu/packages/enlightenment (enlightenment): Update to 0.19.9.

Signed-off-by: Mathieu Lirzin <mthl@openmailbox.org>

* gnu/packages/enlightenment.scm (emotion-generic-players):
  Update to 1.15.0.

Signed-off-by: Mathieu Lirzin <mthl@openmailbox.org>

* gnu/packages/enlightenment.scm (evas-generic-loaders):
  Update to 1.15.0.

Signed-off-by: Mathieu Lirzin <mthl@openmailbox.org>

* gnu/packages/enlightenment.scm (elementary): Update to 1.15.1.

Signed-off-by: Mathieu Lirzin <mthl@openmailbox.org>

* gnu/packages/enlightenment.scm (efl): Update to 1.15.1.

Signed-off-by: Mathieu Lirzin <mthl@openmailbox.org>

* gnu/packages/enlightenment.scm (terminology): Update to 0.9.0.

Signed-off-by: Mathieu Lirzin <mthl@openmailbox.org>

* gnu/packages/ncdu.scm (ncdu): Update to 1.11.

Signed-off-by: Mathieu Lirzin <mthl@openmailbox.org>

This reverts commit 41996f22.

This reverts commit e4c3e2cd.

* gnu/packages/databases.scm (bdb): Build with "--enable-cxx", which causes
  HAVE_CXX_STDHEADERS to be defined in db_cxx.h in the output.

* gnu/packages/databases.scm (bdb): Fix indentation.

* gnu/packages/emacs.scm (emacs-debbugs): New variable.

* gnu/packages/wm.scm (ghc-xmonad-contrib): New variable.

Signed-off-by: Eric Bavier <bavier@member.fsf.org>

* gnu/packages/wm.scm (xmonad): New variable.

Co-authored-by: Eric Bavier <bavier@member.fsf.org>