gnu: agg: Add explanatory comment to the patch.

* gnu/packages/patches/agg-am_c_prototype.patch: Add comment.

gnu: Add agg.

* gnu/packages/graphics.scm (agg): New variable.
* gnu/packages/patches/agg-am_c_prototype.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.

gnu: pavucontrol: Work around segmentation fault.

* gnu/packages/patches/pavucontrol-sigsegv.patch: New file.
* gnu/packages/pulseaudio.scm (pavucontrol)[source]: Use it.
* gnu-system.am (dist_patch_DATA): Add it.

pulseaudio: Update to 6.0; add dependency on eudev.

* gnu/packages/pulseaudio.scm (pulseaudio)[source]: Update to 6.0.
  [arguments]: Pass --with-udev-rules-dir.
  [inputs]: Add eudev.

gnu: bash-completion: Search for completion modules in profiles.

* gnu/packages/patches/bash-completion-directories.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/bash.scm (bash-completion)[source]: Use it.

gnu: icecat: Update to 31.5.0.

* gnu/packages/patches/icecat-CVE-2015-0822.patch,
  gnu/packages/patches/icecat-CVE-2015-0827-pt-1.patch,
  gnu/packages/patches/icecat-CVE-2015-0827-pt-2.patch,
  gnu/packages/patches/icecat-CVE-2015-0827-pt-3.patch,
  gnu/packages/patches/icecat-CVE-2015-0831-pt-1.patch,
  gnu/packages/patches/icecat-CVE-2015-0831-pt-2.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-01.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-02.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-03.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-04.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-05.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-06.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-07.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-08.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-09.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-10.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-11.patch: Remove files.
* gnu-system.am (dist_patch_DATA): Remove them.
* gnu/packages/gnuzilla.scm (icecat): Update to 31.5.0.  Remove patches.
  Add 'nspr', 'nss', and 'cairo' to inputs.  Add configure flags to use
  those system libraries.

gnu: nss: Include -L$libdir in output of "nss-config --libs".

* gnu/packages/patches/nss-pkgconfig.patch (nss-config): Include -L$libdir in
  output of "nss-config --libs".

gnu: Add calibre.

* gnu/packages/ebook.scm (calibre): New variable.
* gnu/packages/patches/calibre-drop-unrar.patch: New file.
* gnu-system.am (dist_patch_DATA): Register patch.

gnu: gnunet: Update to 0.10.1.

* gnu/packages/gnunet.scm (gnunet): Update to 0.10.1.
  Adapt environment variable GNUNET_PREFIX to new use.
  Disable parallel tests.
  Disable tests until a failure is fixed.
* gnu/packages/patches/gnunet-fix-scheduler.patch,
  gnu/packages/patches/gnunet-fix-tests.patch: Delete patch files.
* gnu-system.am (dist_patch_DATA): Unregister patches.

gnu: valgrind: Fix build against glibc 2.21

* gnu/packages/patches/valgrind-glibc-2.21.patch: New file.
* gnu-system.am (dist_patch_DATA): Add patch.
* gnu/packages/valgrind.scm (valgrind): Apply patch.

gnu: grub: Add patch to fix new version of freetype

* gnu/packages/patches/grub-freetype.patch: New file.
* gnu-system.am (dist_patch_DATA): Add the patch.
* gnu/packages/grub.scm (grub): Apply new patch.

gnu: lftp: Don't save unknown SSH host fingerprints to known_hosts by default.

* gnu/packages/patches/lftp-dont-save-unknown-host-fingerprint.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/ftp.scm (lftp): Add patch.

gnu: Add zathura.

* gnu/packages/pdf.scm (zathura): New variable.
* gnu/packages/patches/zathura-plugindir-environment-variable.patch: New file.
* gnu-system.am: Add it.

Merge branch 'core-updates'.

gnu: Add crossmap.

* gnu/packages/bioinformatics.scm (crossmap): New variable.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.

Merge branch 'master' into core-updates

gnu: grep: Apply fix for CVE-2015-1345.

* gnu/packages/patches/grep-CVE-2015-1345.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/base.scm (grep): Add patch.

gnu: icecat: Apply fixes for CVE-2015-{0822,0827,0831,0836}.

* gnu/packages/patches/icecat-CVE-2015-0822.patch,
  gnu/packages/patches/icecat-CVE-2015-0827-pt-1.patch,
  gnu/packages/patches/icecat-CVE-2015-0827-pt-2.patch,
  gnu/packages/patches/icecat-CVE-2015-0827-pt-3.patch,
  gnu/packages/patches/icecat-CVE-2015-0831-pt-1.patch,
  gnu/packages/patches/icecat-CVE-2015-0831-pt-2.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-01.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-02.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-03.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-04.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-05.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-06.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-07.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-08.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-09.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-10.patch,
  gnu/packages/patches/icecat-CVE-2015-0836-pt-11.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/gnuzilla.scm (icecat)[source]: Add patches.

gnu: Fix luajit installation

* gnu/packages/lua.scm (luajit): Apply 2 patches.
* gnu-system.am (dist_patch_DATA): Register 2 patches.
* gnu/packages/patches/luajit-no_ldconfig.patch: New file.
* gnu/packages/patches/luajit-symlinks.patch: New file.

gnu: Add OpenEXR and IlmBase.

* gnu/packages/graphics.scm (ilmbase, openexr): New variables.
* gnu/packages/patches/openexr-missing-samples.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.