gnu: orfm: Update to 0.5.3.

* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.

gnu: Add ruby-bio-commandeer.

* gnu/packages/ruby.scm (ruby-bio-commandeer): New variable.

gnu: Add ruby-systemu.

* gnu/packages/ruby.scm (ruby-systemu): New variable.

gnu: julia: Update to 0.4.3.

* gnu/packages/julia.scm (julia): Update to 0.4.3.
(libuv-julia): Update to 07730c4bd595.

gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605].

* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1.

gnu: samtools: Update to 1.3.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.

gnu: skribilo: Update to 0.9.3.

* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3.
[native-inputs]: New field.

gnu: boost: Update to 1.60.0.

* gnu/packages/boost.scm (boost): Update to 1.60.0.
  [source]: Remove patch.
* gnu/packages/patches/boost-mips-avoid-m32.patch: Delete patch
* gnu-system.am (dist_patch_DATA): Remove patch.

Also fix dependent packages:

* gnu/packages/patches/csound-header-ordering.patch: New patch.
* gnu/packages/audio.scm (csound)[source]: Use it.
  [arguments]: Add 'set-flags phase.
* gnu/packages/patches/libcmis-fix-test-onedrive.patch: New patch.
* gnu/packages/libreoffice.scm (libcmis)[source]: Use it.
  (libreoffice)[arguments]: Add LDFLAGS to #:configure-flags.
  (librevenge)[inputs]: Move boost from here...
  [propogated-inputs]: to here.
  [arguments]: Add LDFLAGS to #:configure-flags.
* gnu/packages/patches/openimageio-boost-1.60.patch: New patch.
* gnu/packages/graphics.scm (openimageio): Use it.
* gnu-system.am (dist_patch_DATA): Add patches.

gnu: boost: Use modify-phases.

* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.

gnu: sudo: Add fix for CVE-2015-5602.

* gnu/packages/patches/sudo-CVE-2015-5602.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/admin.scm (sudo)[source]: Add patch.

gnu: global: Use modify-phases syntax.

* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.

gnu: global: Update to 6.5.2.

* gnu/packages/code.scm (global): Update to 6.5.2.

gnu: icedtea-6: Fix directory name in "unpack" phase.

* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory
  prefix in the "unpack" phase to "icedtea6-".

gnu: linux-libre: Update to 4.4.

* gnu/packages/linux.scm (linux-libre): Update to 4.4.
* gnu/packages/linux-libre-i686.conf,
  gnu/packages/linux-libre-x86_64.conf: Update from
  <https://jxself.org/git/kernel-configs.git>.

gnu: Add fxtract.

* gnu/packages/bioinformatics.scm (fxtract): New variable.

gnu: youtube-dl: Update to 2016.01.09.

* gnu/packages/video.scm (youtube-dl): Update to 2016.01.09.

gnu: gp2c: Update to 0.0.9pl5.

* gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5.

gnu: texlive: Use modify-phases syntax.

* gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases
  syntax.

gnu: man-pages: Update to 4.04.

* gnu/packages/man.scm (man-pages): Update to 4.04.
[source]: Add alternate location.

gnu: bedtools: Update to 2.25.0.

* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[source]: Remove patch merged upstream.
[arguments]: Use 'modify-phases'.  Remove
'patch-makefile-SHELL-definition' phase.
* gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.