* gnu/packages/music.scm (hydrogen): Update to 0.9.6.1.
[build-system]: Switch to cmake-build-system.
[arguments]: Enable configure and tests, remove custom phases.
[native-inputs]: Remove python-2, scons. Add cppunit.
[inputs]: Add libarchive, lrdf.

* gnu/packages/bioinformatics.scm (htseq)[inputs]: Add "python2-pysam".

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

* gnu/packages/augeas.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.

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

* gnu/packages/gps.scm (gpsbabel): Update to 1.5.2.
[inputs]: Remove qt-4, add qt.

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

* gnu/packages/engineering.scm (librecad): Update to 2.0.9.
[inputs]: Use qt instead of qt-4.

* gnu/packages/admin.scm (iftop)[license]: Correct 'gpl3' to 'gpl2+'.

* gnu/packages/audio.scm (shntool)[license]: Correct 'gpl3+' to 'gpl2+'
and add 'x11'.

* gnu/packages/games.scm (pioneers)[license]: Correct 'gpl3+' to 'gpl2+'.

* gnu/packages/games.scm (pioneers): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

* gnu/packages/dav.scm (vdirsyncer): Update to 0.9.0.

* gnu/packages/python.scm (python-click-log): Update to 0.1.3.

* gnu/packages/python.scm (python-atomicwrites): Update to 0.1.9.

* gnu/packages/python.scm (python-lxml, python2-lxml): Update to 3.5.0.
[source]: Use pypi-uri.

* gnu/packages/xdisorg.scm (redshift): Update to 1.11.

* gnu/packages/python.scm (python-sqlalchemy): Update to 1.0.12.

* gnu/packages/parallel.scm (slurm): New variable.
* gnu/packages/patches/slurm-configure-remove-nonfree-contribs.patch:
  New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/parallel.scm: Introduce license name space.

Co-authored-by: Andreas Enge <andreas@enge.fr>

* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3.

*gnu/packages/polkit.scm (polkit-qt)[propagated-inputs]: Use qt.

* gnu/packages/version-control.scm (bazaar): Update to 2.7.0.

* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.32.3.

* gnu/packages/admin.scm (audit): New variable.

* gnu/packages/dictionaries.scm (vera): Update to 1.23.

* gnu/packages/nano.scm (nano): Update to 2.5.2.

* gnu/packages/finance.scm (bitcoin-core): Update to 0.11.2.
[native-inputs]: Use python-2 instead of python-wrapper.

* gnu/packages/owncloud.scm (owncloud-client): Update to 2.1.1.

* gnu/packages/bioinformatics.scm (vsearch): Update to 1.10.0.
[origin]: Adapt to changes in bundling of cityhash.

* gnu/packages/textutils.scm (cityhash)[arguments]: Install citycrc.h.
[version]: Use standardised format, increment to 1.1-2.

* gnu/packages/fontutils.scm (graphite2): Update to 1.3.5.
  [source, home-page]: Update to reflect upstream move to github.

Note: The previous fix for CVE-2015-7805 was incomplete.

* gnu/packages/patches/libsndfile-CVE-2014-9496.patch,
  gnu/packages/patches/libsndfile-CVE-2015-7805.patch: Delete files.
* gnu-system.am (dist_patch_DATA): Remove them.
* gnu/packages/pulseaudio.scm (libsndfile): Update to 1.0.26.
  [source]: Remove patches.

* gnu/packages/gnupg.scm (libgcrypt): Update to 1.6.5.

Reported by Tobias Geerinckx-Rice <tobias.geerinckx.rice@gmail.com>

* gnu/packages/linux.scm (btrfs-progs)[license]: Add GPL2 to list of licenses.

* gnu/packages/fonts.scm (font-terminus): Update to 4.40.

Signed-off-by: Leo Famulari <leo@famulari.name>

* gnu/packages/python.scm (python-ly): Update to 0.9.3.

* gnu/packages/lxqt.scm (libqtxdg, liblxqt, lxqt-common)
  (lxqt-session)[source]: Use HTTPS URLs.

* gnu/packages/openbox.scm (openbox): Update to 3.6.1.

* gnu/packages/databases.scm (postgresql): Update to 9.3.11.

* gnu/packages/gnome.scm (baobab): New variable.