gnu: bash: Do not retain dependency on Coreutils.

Previously the "include" output of BASH-FINAL would refer to
'bootstrap-binaries' via 'Makefile.inc'.

* gnu/packages/bash.scm (bash)[arguments]: In 'move-development-files'
phase, remove absolute file name of 'install' from the 'INSTALL'
variable in 'Makefile.inc'.
* gnu/packages/commencement.scm (bash-final)[arguments]: Pass
 #:disallowed-references.

gnu: coreutils: Fix cross-compilation.

* gnu/packages/patches/coreutils-fix-cross-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/base.scm (coreutils)[source]: Use it.

gnu: mupdf, cups-filters: Incorporated grafted changes.

* gnu/packages/pdf.scm (mupdf)[replacement]: Remove field.
[source]: Add 'mupdf-mujs-CVE-2016-10132.patch' and
'mupdf-mujs-CVE-2016-10133.patch'.
(mupdf/fixed): Remove variable.
* gnu/packages/cups.scm (cups-filters)[replacement]: Remove field.
(mupdf/fixed-instead-of-mupdf),(cups-filters/fixed): Remove variables.

utils: Add helper method to make files writable.

* gnu/build/activation.scm (make-file-writable): Move this to ...
* guix/build/utils.scm (make-file-writable): ... here. Export it.
* guix/build/gnu-build-system.scm (strip): Use it.

gnu: pkg-config: Update to 0.29.1.

* gnu/packages/pkg-config.scm (%pkg-config): Update to 0.29.1.
[home-page]: Use HTTPS.

build-system/gnu: Add 'reset-gzip-timestamps' phase.

* guix/build/gnu-build-system.scm (reset-gzip-timestamps): New
procedure.
(%standard-phases): Add it.

utils: Add 'gzip-file?' and 'reset-gzip-timestamp'.

* guix/build/utils.scm (%gzip-magic-bytes): New variable.
(gzip-file?, reset-gzip-timestamp): New procedures.

build-system/gnu: 'strip' phase now skips symlinks.

This avoids a situation where the "debug" output would contain separate
(and different) .debug files for "libfoo.so" and "libfoo.so.0.0", even
though "libfoo.so" is actually a symlink to "libfoo.so.0.0".

* guix/build/gnu-build-system.scm (strip): Remove 'file-exists?' call in
'for-each' lambda.  Pass a predicate to 'find-files' to restrict the
result to regular files.

gnu: gnutls: Update to 3.5.8.

* gnu/packages/tls.scm (gnutls): Update to 3.5.8.

gnu: gd: Incorporate grafted changes.

* gnu/packages/gd.scm (gd)[replacement]: Remove field.
[source]: Update to 2.2.4. Remove patches 'gd-CVE-2016-7568.patch' and
'gd-CVE-2016-8670.patch'.
[arguments]: New field.
(gd-2.2.4): Remove variable.
* gnu/packages/patches/gd-CVE-2016-7568.patch,
gnu/packages/patches/gd-CVE-2016-8670.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.

gnu: lcms: Incorporate grafted patch.

* gnu/packages/ghostscript.scm (lcms)[replacement]: Remove field.
[source]: Add patch 'lcms-fix-out-of-bounds-read.patch'.
(lcms/fixed): Remove variable.

gnu: tcsh: Incorporate grafted patch.

* gnu/packages/shells.scm (tcsh)[replacement]: Remove field.
[source]: Add patch 'tcsh-fix-out-of-bounds-read.patch'.
(tcsh/fixed): Remove variable.

gnu: openjpeg: Incorporate grafted changes.

* gnu/packages/image.scm (openjpeg)[replacement]: Remove field.
[source]: Update to 2.1.2. Add patches
'openjpeg-CVE-2016-9850-CVE-2016-9851.patch' and
'openjpeg-CVE-2016-9572-CVE-2016-9573.patch'.
(openjpeg-1)[replacement]: Remove field.
(openjpeg-2.1.2): Remove variable.

gnu: libtiff: Incorporate grafted patches.

* gnu/packages/image.scm (libtiff)[replacement]: Remove field.
[source]: Add patches from libtiff/fixed.
(libtiff/fixed): Remove variable.

gnu: libpng: Incorporate grafted patch.

* gnu/packages/image.scm (libpng)[replacement]: Remove field.
[source]: Add patch 'libpng-CVE-2016-10087.patch'.
(libpng-1.2)[replacement]: Remove field.
(libpng/fixed): Remove variable.

gnu: curl: Incorporate grafted changes.

* gnu/packages/curl.scm (curl)[replacement]: Remove field.
(curl-7.52.1): Remove variable.

gnu: libxslt: Incorporate grafted patch.

* gnu/packages/xml.scm (libxslt)[replacement]: Remove field.
[source]: Add patch 'libxslt-CVE-2016-4738.patch'.
(libxslt/fixed): Remove variable.

gnu: libxml2: Incorporate grafted patches.

* gnu/packages/xml.scm (libxml2)[replacement]: Remove field.
[source]: Add patches 'libxml2-CVE-2016-4658.patch' and
'libxml2-CVE-2016-5131.patch'.
(python-libxml2)[replacement]: Remove field.
(libxml2/fixed): Remove variable.

Merge branch 'master' into core-updates

gnu: Add stunnel.

* gnu/packages/web.scm (stunnel): New variable.

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