activation: Don't create unneeded "/var/guix/gcroots/etc-directory".

* gnu/build/activation.scm (activate-etc): Don't create
  "/var/guix/gcroots/etc-directory".
guix: scripts: Parse $GUIX_BUILD_OPTIONS separately.

Appending to "raw" args broke optional parameters in 'guix package -I'
and 'guix package -A', and possibly other places.  Therefore, switch to
parsing each set of options on its own and append resulting alists
together afterwards.

* guix/scripts/archive.scm (parse-options-from): Rename from
  (parse-options) and add explicit argument.  New form of (parse-options)
  using its old algorithm via -from function.
* guix/scripts/build.scm: Ditto.
* guix/scripts/environment.scm: Ditto.
* guix/scripts/package.scm: Ditto.
* guix/scripts/system.scm: Ditto.
* tests/guix-package.sh: Add test.
* doc/guix.texi (Invoking guix build): Make it clear that the options
  are parsed independently.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
guix system: Fix typo affecting 'guix system init'.

Fixes <http://bugs.gnu.org/19279>.
Fixes a regression introduced in cc7fa59.
Reported by Tomas Cech <tcech@suse.cz>.

* guix/scripts/system.scm (install): Fix order of arguments to 'lift'
  and 'lift2'.
gnu: Add libyubikey and ykclient.

* gnu/packages/yubico.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
gnu: fish: Use /etc as sysconfdir.

* gnu/packages/fish.scm (fish) [arguments]: Add #:configure-flags.
  [origin]: Add snippet.
gnu: tzdata: Update to 2014j.

* gnu/packages/base.scm (tzdata): Update to 2014j.
gnu: python2-py2cairo: Fix 'license' field.

* gnu/packages/gtk.scm (python2-py2cairo)[license]: Change to a list of
  <license> (was a list of symbols.)
nls: Update 'eo' translation.
doc: Give example uses of 'deco'.

Suggested by Sleep_Walker on #guix.

* doc/guix.texi (Services): Add 'deco' examples.
system: Add 'man-db' to '%base-packages'.

Suggested by Tsutsukakushi on #guix.

* gnu/system.scm (%base-packages): Add MAN-DB.
gnu: linux-libre: Update to 3.18

* gnu/packages/linux.scm (linux-libre): Update to version 3.18.
gnu: atlas: Remove MIPS from 'supported-systems'.

* gnu/packages/maths.scm (atlas): Drop support for "mips64el-linux".
build-system/python: Add handling of 'propagated-inputs' in
'package-with-explicit-python'.

* guix/build-system/python.scm (package-with-explicit-python): Add mapping for
  'propagated-inputs'.
linux-initrd: Add the 'virtio_console' module for QEMU guests.

* gnu/system/linux-initrd.scm (base-initrd)[virtio-modules]: Add
  "virtio_console".
gnu: Add socat.

* gnu/packages/socat.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
system: Don't make /boot/grub/grub.cfg a symlink to the store.

This would not work when /boot is a separate partition, as reported by
Nikita Karetnikov <nikita@karetnikov.org> in <http://bugs.gnu.org/19220>.
This fixes a regression introduced in 39d1f82.

* gnu/build/install.scm (install-grub): Copy GRUB.CFG instead of
  symlinking it, as was the case before 39d1f82.
* gnu/build/vm.scm (register-grub.cfg-root): Add 'grub.cfg' parameter.
  Make it a permanent GC root instead of an indirect GC root.
  (initialize-hard-disk): Adjust accordingly.
* guix/scripts/system.scm (install-grub*): Replace use of
  'add-indirect-root' by the addition of a permanent GC root in
  %GC-ROOTS-DIRECTORY.
substitute-binary: Add missing newline in download progress report.

Fixes <http://bugs.gnu.org/19313>.
Reported by rekado <rekado@elephly.net>.

* guix/scripts/substitute-binary.scm (guix-substitute-binary)
  <--substitute>: Add 'newline' call.
doc: Explain how to set the ownership and permissions of /gnu/store.

Fixes <http://bugs.gnu.org/19316>.
Reported by rekado <rekado@elephly.net>.

* doc/guix.texi (Build Environment Setup): Show commands to set the
  ownership and permissions of /gnu/store.
Thank rekado.
build: Make sure the installed 'config.go' is newer than 'config.scm'.

Fixes <http://bugs.gnu.org/19317>.
Reported by rekado <rekado@elephly.net>.

* gnu-system.am (install-data-hook): Rename to...
  (set-bootstrap-executable-permissions): ... this.
* Makefile.am (install-data-hook): New target.