packages: Remove support for PACKAGE-VERSION deprecated syntax.

This syntax had been deprecated since 2016-02-28.

* gnu/packages.scm (%find-package): Remove #:fallback? parameter and handling.
* tests/guix-build.sh: Remove test for "time-1.7" syntax.
* doc/guix.texi (Invoking guix lint): Update 'guix lint' output in example.

refresh: Report packages using the "@" syntax.

* guix/scripts/refresh.scm (list-dependents)[full-name]: New procedure.
Use 'full-name' instead of 'package-full-name'.
* doc/guix.texi (Invoking guix refresh): Adjust example accordingly.

gnu: vcftools: Update to 0.1.15.

* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.15.

gnu: services: nginx: Fix key verification.

* gnu/services/web.scm (default-nginx-server-config): Fix wrong variable name.

gnu: services: Create logs directory.

* gnu/services/web.scm (nginx-activation): Create logs directory so nginx can
log its startup messages before it loads its configuration.

gnu: services: nginx: Test certificate presence.

* gnu/services/web.scm (default-nginx-server-config): Test certificate
presence when https is requested at configure time.

gnu: neomutt: Update to 20170428.

* gnu/packages/mail.scm (neomutt): Update to 20170428.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>

gnu: emacs-mu4e-alert: Update to 1.0.

* gnu/packages/emacs.scm (emacs-mu4e-alert): Update to 1.0.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>

gnu: Add gcc-vc4.

Fixes <https://bugs.gnu.org/26541>.

* gnu/packages/bootstrap.scm (glibc-dynamic-linker): Add vc4-elf.
* gnu/packages/embedded.scm (gcc-vc4): New variable.

gnu: guile-git: Update to revision 2.

* gnu/packages/guile.scm (guile-git): Update to revision 2.
[arguments]: remove "ccache -> site-ccache" substitution because it
has been ported upstream.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>

gnu: python-llfuse: Update to 1.2.

* gnu/packages/python.scm (python-llfuse, python2-llfuse): Update to 1.2.

gnu: fuse: Update to 2.9.7.

* gnu/packages/linux.scm (fuse): Update to 2.9.7.

gnu: radicale: Update to 1.1.2 [fixes CVE-2017-8342].

* gnu/packages/dav.scm (radicale): Update to 1.1.2.

Revert "gnu: Move netsurf to web-browsers.scm."

This change caused building Guix to fail with:

 393: 1 [eval #<memoized glib-or-gtk-build-system> (# "3.6" "netsurf" . #)]

This reverts commit a39ee1accb384fa4747a2a14d44616557419087f.

gnu: Move netsurf to web-browsers.scm.

* gnu/packages/web.scm: Move netsurf...
* gnu/packages/web-browsers.scm: ...here.

gnu: glibc/linux: Fix build of glibc-intermediate.

This is a follow-up to commit b2fd8f63679aa4f244c36fdca62f23c00b8eded9.

* gnu/packages/base.scm (glibc/linux)[arguments]: Take patch from either
native-inputs or just inputs; fix syntax error; report errors on patch
failure.

gnu: femtolisp: Remove aarch64-linux from supported-architectures.

* gnu/packages/lisp.scm (femtolisp)[supported-systems]: Remove
aarch64-linux from supported-systems.

gnu: Add netcdf-fortran.

* gnu/packages/maths.scm (netcdf-fortran): New variable.

gnu: jemalloc: Disable transparent huge pages on non-Intel systems.

* gnu/packages/jemalloc.scm (jemalloc)[arguments]: On non-Intel systems
add '--disable-thp' to #:configure-flags. Adjust #:phases to remove
offending test which incorrectly tests transparent huge pages.

python-sphinxcontrib-programoutput: Update to 0.10.

* gnu/packages/python.scm (python-sphinxcontrib-programoutput): Update to 0.10.