* gnu/packages/ebook.scm (calibre): Update to 2.49.0.

* gnu/packages/cross-base.scm (cross-gcc-arguments)[arguments]: Disable
  building libstdc++-v3 and enable building C++ compiler.

* gnu/packages/music.scm (qtractor): New variable.

* gnu/packages/music.scm (yoshimi): Update to 1.3.8.2.

* gnu/packages/tor.scm (privoxy): Update to 3.0.24.

* gnu/packages/tor.scm (tor): Update to 0.2.7.6.

* gnu/packages/version-control.scm (myrepos): Update to 1.20160123.

* gnu/packages/nano.scm (nano): Update to 2.5.1.

* gnu/build/linux-container.scm (unprivileged-user-namespace-supported?): Only
  read and check the first character, to cope with a possible newline in the
  (pseudo-)file.

These packages should be updated together.

* gnu/packages/tls.scm (letsencrypt): Update to 0.2.0.
(acme): Update to 0.2.0.

* gnu/packages/mail.scm (claws-mail): Update to 3.13.2.

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

* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.

* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".

* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
  syntax.

* gnu/packages/linux.scm (fuse): Update to 2.9.5.

* gnu/packages/debug.scm (american-fuzzy-lop): Update to 1.96b.
  [arguments]: Create symbolic link to custom qemu, rather than copying.

Fixes regression introduced in 06da1a6b.

* gnu/packages/debug.scm (american-fuzzy-lop)[qemu]: Override inherited
  #:configure-flags.

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

This reverts commit 45da8c6d.

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

* tests/lint.scm: Add call to 'unsetenv' to remove 'http_proxy'.
* tests/publish.scm: Likewise.

* doc/guix.texi (Locales): Add missing 's'.

Fixes <http://bugs.gnu.org/22281>.
Reported by Christopher Allan Webber <cwebber@dustycloud.org>.

* gnu/system/grub.scm (eye-candy): Add 'root-fs' parameter.  Replace
'search --file' command in the output with whatever 'grub-root-search'
returns.
(grub-root-search): New procedure.
(grub-configuration-file): Add 'store-fs' parameter.  Use
'grub-root-search' instead of hard-coded 'search --file' commands.
* gnu/system.scm (store-file-system,
operating-system-store-file-system): New procedures.
(operating-system-grub.cfg): Use it, and adjust call to
'grub-configuration-file'.
* tests/system.scm: New file.
* Makefile.am (SCM_TESTS): Add it.

* gnu/packages/video.scm (ffmpeg): Update to 2.8.5.

* gnu/packages/messaging.scm (gajim): Update to 0.16.5.
  [arguments]: Disable tests.

* gnu/packages/dns.scm (bind-utils)[arguments]: Build and install
  "nsupdate" executable.

* gnu/packages/dns.scm (bind-utils)[arguments]: Generalize "build" and
  "install" phases.

* gnu/packages/dns.scm (bind-utils): Use "modify-phases" syntax.

* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.

* gnu/packages/audio.scm (libxmp): Update to 4.3.10.

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

* guix/licenses.scm (mpl1.0): New variable.

* gnu/packages/bittorrent.scm (transmission-remote-cli): New variable.

Suggested by David Thompson <dthompson2@worcester.edu>
at <http://bugs.gnu.org/22402>.

* doc/guix.texi (Binary Installation): Explain how to make the Info
manual visible.

Suggested by <swedebugia@riseup.net>.

* doc/guix.texi (Using the Configuration System): Add
@unnumberedsubsubsec.  Explain how to remove services from a list.
Mention (gnu system).

* gnu/services/avahi.scm: Export 'avahi-service-type'.

* gnu/packages/admin.scm (isc-dhcp): Update bundled bind to 9.9.8-P3.

* gnu/packages/dns.scm (bind-utils): Update to 9.10.3-P3.

* gnu/packages/patches/linux-libre-CVE-2016-0728.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/linux.scm (linux-libre)[source]: Add patch.