gnu: ruby-2.2.7: Fix CVE-2017-{0899,0900,0901,0902}.

* gnu/packages/patches/ruby-2.2.7-rubygems-2613-ruby22.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/ruby.scm (ruby-2.2.7)[source]: Use it.

gnu: ruby-2.3.4: Fix CVE-2017-{0899,0900,0901,0902}.

* gnu/packages/patches/ruby-2.3.4-rubygems-2613-ruby23.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/ruby.scm (ruby-2.3.4)[source]: Use it.

gnu: ruby-2.4.1: Fix CVE-2017-{0899,0900,0901,0902}.

* gnu/packages/patches/ruby-rubygems-2612-ruby24.patch,
gnu/packages/patches/ruby-rubygems-2613-ruby24.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/ruby.scm (ruby-2.4.1)[source]: Use them.

gnu: metabat: Update to 2.11.3.

* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3.
[source]: Use git-fetch.  Remove boost-related patch.
* gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: vlc: Fix build and clean up expression.

Commit 3e0c54bf4de0b5e9d77271613287457dbcd64103 touches 'configure.ac' which
in turn regenerates 'po/Makefile.in.in' with the wrong SHELL and breaks
install.  While at it, consolidate the other patching phases and remove
unneeded inputs.

* gnu/packages/video.scm (vlc)[arguments]: Consolidate patching phases into a
'patch-source' phase and run it immediately after unpack.
[native-inputs]: Remove AUTOCONF, AUTOMAKE and LIBTOOL.

gnu: vlc: Recover lost phase.

This is a followup to eb1f2420d5d72bb5d178a744cffb4978c7446286.

* gnu/packages/video.scm (vlc)[arguments]: Run the fix-livemedia-utils-prefix
phase before configure.

gnu: gd: Replace with 2.2.5.

Fixes CVE-2017-6362 and CVE-2017-7890.

* gnu/packages/gd.scm (gd)[replacement]: New field.
(gd-2.2.5): New variable.
* gnu/packages/php.scm (gd-for-php): Remove variable
(php)[inputs]: Replace GD-FOR-PHP with GD-2.2.5.
* gnu/packages/patches/gd-CVE-2017-7890.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: claws-mail: Update to 3.15.1.

* gnu/packages/mail.scm (claws-mail): Update to 3.15.1.

gnu: Add texlive-latex-acmart.

* gnu/packages/tex.scm (texlive-latex-acmart): New variable.

gnu: mbedtls-apache: Update to 2.6.0 [fixes CVE-2017-14032].

* gnu/packages/tls.scm (mbedtls-apache): Update to 2.6.0.

gnu: vlc: Remove obsolete test workaround.

* gnu/packages/video.scm (vlc)[arguments]: Drop ac_cv_c_fast_math from
  #:configure-flags.  Remove related 'bootstrap' phase.

gnu: vlc: Build with modular qt.

* gnu/packages/video.scm (vlc)[inputs]: Remove QT.  Add QTBASE and QTX11EXTRAS.
[arguments]: Add CXXFLAGS=-std=gnu++11 to #:configure-flags.  Add
'fix-qt-include' phase.

gnu: qemu: Update to 2.10.0.

* gnu/packages/patches/qemu-CVE-2017-10664.patch,
gnu/packages/patches/qemu-CVE-2017-10806.patch,
gnu/packages/patches/qemu-CVE-2017-10911.patch,
gnu/packages/patches/qemu-CVE-2017-11334.patch,
gnu/packages/patches/qemu-CVE-2017-11434.patch,
gnu/packages/patches/qemu-CVE-2017-12809.patch:
gnu/packages/patches/qemu-CVE-2017-7493.patch,
gnu/packages/patches/qemu-CVE-2017-8112.patch,
gnu/packages/patches/qemu-CVE-2017-8309.patch,
gnu/packages/patches/qemu-CVE-2017-8379.patch,
gnu/packages/patches/qemu-CVE-2017-8380.patch,
gnu/packages/patches/qemu-CVE-2017-9524.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/virtualization.scm (qemu): Update to 2.10.0.
[source](patches): Remove.

gnu: jsoncpp: Update to 1.8.2.

* gnu/packages/serialization.scm (jsoncpp): Update to 1.8.2.

gnu: multiqc: Update to 1.2.

* gnu/packages/bioinformatics.scm (multiqc): Update to 1.2.
[source]: Remove patches.
[arguments]: Remove to enable tests.
[propagated-inputs]: Add python-spectra, python-requests, python-markdown,
python-lzstring.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: Add python-spectra.

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

gnu: Add python-colormath.

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

gnu: python-jinja2: Update to 2.9.6.

* gnu/packages/python.scm (python-jinja2): Update to 2.9.6.
[arguments]: Add build phase "delete-incompatible-files".

gnu: Add python-lzstring.

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

gnu: hyperrogue: Update to 10.0g.

* gnu/packages/games.scm (hyperrogue): Update to 10.0g.