gnu: Rename module gnutls to tls.

* gnu/packages/gnutls.scm: Rename to...
* gnu/packages/tls.scm: ... this.  Change module name accordingly.
* gnu/packages/{admin.scm, cups.scm, curl.scm, dc.scm, dns.scm, emacs.scm,
  ftp.scm, gnome.scm, gnunet.scm, gnupg.scm, gsasl.scm, lynx.scm,
  mail.scm, messaging.scm, package-management.scm, shishi.scm,
  task-management.scm, version-control.scm, video.scm, vpn.scm,
  webkit.scm, weechat.scm, wget.scm, wine.scm, xml.scm}: Adapt module
  import to new name.
* gnu-system.am (GNU_SYSTEM_MODULES): Rename gnutls module to tls.

gnu: avidemux: Drop version 2.5.

* gnu/packages/video.scm (avidemux-2.5): Delete variable.

gnu: Add prodigal.

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

gnu: shogun: Build with install RPATH.

* gnu/packages/bioinformatics.scm (shogun)[arguments]: Add configure flag to
  build with install RPATH.

gnu: englightenment: Use https URLs.

* gnu/packages/enlightenment.scm (efl, elementary, emotion-generic-players,
  terminology, enlightenment): Use https instead of http since the latter
  redirects to the former.

gnu: enlightenment: Update to 0.19.5.

* gnu/packages/enlightenment.scm (enlightenment): Update to 0.19.5.

gnu: emotion-generic-loaders: Update to 1.14.0.

* gnu/packages/enlightenment.scm (emotion-generic-loaders): Update
  to 1.14.0.

gnu: evas-generic-loaders: Update to 1.14.0.

* gnu/packages/enlightenment.scm (evas-generic-loaders): Update
  to 1.14.0.

gnu: elementary: Update to 1.14.2.

* gnu/packages/enlightenment.scm (elementary): Update to 1.14.2.

gnu: efl: Update to 1.14.2.

* gnu/packages/enlightenment.scm (efl): Update to 1.14.2.

gnu: Add ruby-rake-compiler.

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

gnu: eigen: Update to 3.2.5.

* gnu/packages/algebra.scm (eigen): Update to 3.2.5.

gnu: icecat: Fix CVE-2015-{2722,2724,2728,2733,2735,2736,2738,2739,2740,2743}.

* gnu/packages/patches/icecat-CVE-2015-2722-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-2722-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-2724-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-2724-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-2724-pt3.patch,
  gnu/packages/patches/icecat-CVE-2015-2724-pt4.patch,
  gnu/packages/patches/icecat-CVE-2015-2728-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-2728-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-2733-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-2733-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-2735.patch,
  gnu/packages/patches/icecat-CVE-2015-2736.patch,
  gnu/packages/patches/icecat-CVE-2015-2738.patch,
  gnu/packages/patches/icecat-CVE-2015-2739.patch,
  gnu/packages/patches/icecat-CVE-2015-2740.patch,
  gnu/packages/patches/icecat-CVE-2015-2743.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/gnuzilla.scm (icecat)[source]: Add patches.

gnu: unrtf: Fix download location.

* gnu/packages/unrtf.scm (unrtf): Fix download location.

gnu: r: Replace "atlas" with "openblas".

* gnu/packages/statistics.scm (r)[inputs]: Replace "atlas" with "openblas".

gnu: gnutls: Move man3 pages to "doc" output.

* gnu/packages/gnutls.scm (gnutls)[arguments]: Add #:phases.

gnu: qt-4: Remove reference from "out" to "doc".

* gnu/packages/qt.scm (qt-4)[arguments]: Remove '-docdir' configure flag.
  Add 'move-doc' phase.

gnu: qt-4: Use a more standard directory layout.

* gnu/packages/qt.scm (qt-4)[arguments]: Pass -datadir, -importdir,
  -plugindir, and -translationdir.

gnu: qt-4: Use 'modify-phases'.

* gnu/packages/qt.scm (qt-4)[arguments]: Use 'modify-phases' instead of
  'alist-replace'.

gnu: cups-filter: Install backends and filters under lib/cups.

This ensures that they are stripped during the 'strip' phase, thereby removing
references to GCC and linux-libre-headers that would otherwise be found in
debugging symbols.

* gnu/packages/cups.scm (cups-filters)[source]: Change pkgbackenddir and
  pkgfilterdir to $(PREFIX)/lib/cups/{filter,backend}.
  (cups)[arguments]: Adjust accordingly.