gnu: Update module imports for asciidoc and doxygen.

This is a followup to commit 0573a923def01e54bf104e0015ade44ab42f694f.

* gnu/packages/algebra.scm, gnu/packages/bioinformatics.scm,
gnu/packages/fcitx.scm, gnu/packages/fish.scm,
gnu/packages/freedesktop.scm, gnu/packages/game-development.scm,
gnu/packages/gcc.scm, gnu/packages/graphics.scm, gnu/packages/image.scm,
gnu/packages/kodi.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/messaging.scm,
gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/rdf.scm,
gnu/packages/serialization.scm, gnu/packages/version-control.scm,
gnu/packages/web.scm, gnu/packages/wm.scm, gnu/packages/xdisorg.scm,
gnu/packages/xiph.scm: Change imports of (gnu packages asciidoc) or
(gnu packages doxygen) to (gnu packages documentation).

Merge branch 'gnome-updates'

gnu: linux-libre: Update to 4.5.4.

* gnu/packages/linux.scm (linux-libre): Update to 4.5.4.

gnu: linux-libre-4.4: Update to 4.4.10.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.10.

gnu: linux-libre-4.1: Update to 4.1.24.

* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.24.

gnu: icecat: Update to 38.8.0-gnu1.

* gnu/packages/patches/icecat-CVE-2016-2805.patch,
gnu/packages/patches/icecat-CVE-2016-2807-pt1.patch,
gnu/packages/patches/icecat-CVE-2016-2807-pt2.patch,
gnu/packages/patches/icecat-CVE-2016-2807-pt3.patch,
gnu/packages/patches/icecat-CVE-2016-2807-pt4.patch,
gnu/packages/patches/icecat-CVE-2016-2807-pt5.patch,
gnu/packages/patches/icecat-CVE-2016-2808.patch,
gnu/packages/patches/icecat-CVE-2016-2814.patch,
gnu/packages/patches/icecat-re-enable-DHE-cipher-suites.patch,
gnu/packages/patches/icecat-update-bundled-graphite2.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
* gnu/packages/gnuzilla.scm (icecat): Update to 38.8.0-gnu1.
[source] Remove deleted patches.

gnu: Add NetCDF.

* gnu/packages/maths.scm (netcdf, netcdf-parallel-openmpi): New variables.

gnu: Add Matio.

* gnu/packages/maths.scm (matio): New variable.

gnu: Add h5check.

* gnu/packages/maths.scm (h5check): New variable.

gnu: Add hdf5-openmpi.

* gnu/packages/maths.scm (hdf5-openmpi): New variable.

gnu: hdf5: Have configure honor SOURCE_DATE_EPOCH.

* gnu/packages/patches/hdf5-config-date.patch: New patch.
* gnu/packages/maths.scm (hdf5)[source]: Use it.
* gnu-system.am (dist_patch_DATA): Add it.

gnu: hdf5: Patch output references to zlib.

* gnu/packages/maths.scm (hdf5)[arguments]: Use modify-phases.  Add
'patch-references' phase.

gnu: hdf5: Update to 1.8.17.

* gnu/packages/maths.scm (hdf5): Update to 1.8.17.

gnu: Add HYPRE.

* gnu/packages/maths.scm (hypre, hypre-openmpi): New variables.
* gnu/packages/patches/hypre-doc-tables.patch,
gnu/packages/patches/hypre-ldflags.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.

gnu: Add doc++.

* gnu/packages/documentation.scm (doc++): New variable.
* gnu/packages/patches/doc++-include-directives.patch,
  gnu/packages/patches/doc++-segfault-fix.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.

gnu: Move asciidoc and doxygen to new module.

* gnu/packages/asciidoc.scm (asciidoc): Move this...
* gnu/packages/doxygen.scm (doxygen): ...and this...
* gnu/packages/documentation.scm: ...to here.  New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add accordingly.

gnu: claws-mail: Add shared-mime-info input.

* gnu/packages/mail.scm (claws-mail)[inputs]: Add shared-mime-info.
[arguments]: Add 'patch-mime' phase.

gnu: nmap: Update to 7.12.

* gnu/packages/admin.scm (nmap): Update to 7.12.

gnu: tinc: Update to 1.0.28.

gnu: openvpn: Update to 2.3.9.

* gnu/packages/vpn.scm (openvpn): Update to 2.3.9.