* guix/scripts/refresh.scm (%options, show-help): Add --expression.
(guix-refresh): Honor it.
* doc/guix.texi (Invoking guix refresh): Document it.

* guix/scripts/download.scm (guix-download)[parse-option]: Call 'leave'
when passed an extra argument.
* tests/guix-download.sh: Add test.

Fixes <http://bugs.gnu.org/21991>.
Reported by Jan Synáček <jan.synacek@gmail.com>.

* guix/scripts/download.scm (guix-download): Call 'leave' when OPTS does
not contain an 'argument' key.

* gnu/packages/textutils.scm (enca): Add file-name field to source.

* gnu/packages/textutils.scm (recode): Add file-name field to source.

* gnu/packages/firmware.scm (ath9k-htc-firmware)[source](file-name): New
field.
* gnu/packages/gnunet.scm (guile-gnunet)[source](file-name): New field.
* gnu/packages/guile.scm (guile-next)[source](file-name): New field.
(guile-minikanren)[source](file-name): New field
(guile-gdbm-ffi)[source](file-name): New field.
* gnu/packages/ssh.scm (guile-ssh)[source](file-name): New field.

Reported by Mathieu Lirzin <mthl@gnu.org> at
<http://lists.gnu.org/archive/html/guix-devel/2015-11/msg00585.html>.

* emacs/guix-backend.el (guix-start-repl): Expand 'guix-load-path' to
  avoid a potentially relative directory name in Guile %load-path.

* guix/ftp-client.scm (ftp-open): Change default #:port to "ftp".
* guix/scripts/lint.scm (probe-uri): Remove 'port' parameter to
'ftp-open'.

* guix/ftp-client.scm (ftp-open): Change to use 'match' instead of
car/cdr, and fix off-by-one (was '(null? addresses)' instead of
'(null? (cdr addresses))'.)

* doc/contributing.texi (Building from Git): Mention 'guix environment
guix'.  Remove outdated description of ./bootstrap.  Clarify a few
things.

Fixes <http://bugs.gnu.org/21958>.

* guix/scripts/environment.scm (status->exit-code): New procedure.
(exit/status, primitive-exit/status): Use it.
* tests/guix-environment-container.sh: Add test.

Fixes <http://bugs.gnu.org/21410>.
Reported by Alex Vong <alexvong1995@gmail.com>.

* tests/guix-environment-container.sh: Exit with 77 when
'((@@ (guix scripts environment) assert-container-features))' fails.

* doc/contributing.texi (Building from Git): Remove extra "See" and use
@xref instead of @pxref.

* gnu/packages/version-control.scm (tig): Update to 2.1.1.

* gnu/packages/version-control.scm (cvs)[arguments]: add configure flag
  --with-exernal-zlib.

* gnu/packages/nano.scm (nano): Update to 2.4.3.

* guix/scripts/refresh.scm (all-packages, list-dependents): New
procedures.
(guix-refresh): Use it.

* guix/graph.scm (%node-edges, node-edges, node-back-edges)
(node-transitive-edges): New procedures.
* tests/graph.scm ("node-edges")
("node-transitive-edges + node-back-edges"): New tests.

* guix/scripts/graph.scm (<node-type>, <graph-backend>, emit-prologue)
(emit-epilogue, emit-node, emit-edge, %graphviz-backend, export-graph):
Move to...
* guix/graph.scm: ... here.  New file.
* guix/scripts/system.scm, tests/graph.scm: Use it.
* Makefile.am (MODULES): Add it.

* gnu/packages/disk.scm (parted): Update to 3.2.
[inputs]: Add lvm2 and remove check.  Replace readline-6.2 with its
latest version.
[native-inputs]: Add perl and python for the tests.
[arguments]: Use `modify-phases' and adapt to the new tests.
[home-page]: Use https.

* gnu/packages/qemu.scm (qemu): Exchange with former QEMU-HEADLESS.
(qemu-headless): Rename to...
(qemu-minimal): ... this.  New variable.  Pass --target-list.
* gnu/packages/debug.scm (qemu-2.3.0): Inherit from QEMU-MINIMAL.
* gnu/packages/grub.scm (qemu-for-tests): Likewise.
* gnu/system/vm.scm (expression->derivation-in-linux-vm, qemu-image):
Update to name change.

Reported by marusich on #guix.

* doc/contributing.texi (The Perfect Setup): Wrap modifying
  'geiser-guile-load-path' into 'with-eval-after-load'.

* gnu/packages/animation.scm (synfigstudio): New variable.

* gnu/packages/animation.scm (synfig): New variable.
* gnu/packages/patches/synfig-build-fix.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.

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

* gnu/packages/video.scm (mlt): New variable.

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

* gnu/packages/maths.scm (slepc): Update to 3.6.2.
  [arguments]: Append "/lib" to arpack configure flag.  Use 'inputs'
  rather than '%build-inputs' in 'configure phase.

* gnu/packages/maths.scm (petsc): Update to 3.6.2.

* gnu/packages/maths.scm (mumps): Update to 5.0.1.

* gnu/packages/mpi.scm (openmpi): Update to 1.10.1.
  [arguments]: Remove now-unsupported configure flags.  Add
  --enable-builtin-atomics.  Remove development-oriented
  --enable-debug.

* gnu/packages/mpi.scm (hwloc): Update to 1.11.1.
  [source]: Remove patch.
* gnu/packages/patches/hwloc-gather-topology-lstopo.patch: Delete it.
* gnu-system.am (dist_patch_DATA): Remove it.

* gnu/packages/audio.scm (guitarix): Update to 0.34.0.
[source]: Remove patch.
[inputs]: Add webkitgtk/gtk+-2.
* gnu/packages/patches/guitarix-c++11: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.

* gnu/services/base.scm (gpm-dmd-service): s/dmd/gpm/

* gnu/packages/games.scm (emulation-station): New variable.

* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
[source]: Add file-name field, remove patches.
[arguments]: Remove unused build phases, add make flags.
[inputs]: Add smithlab-cpp.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
  file.
* gnu-system.am (dist_patch_DATA): Remove them.

* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.

* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing
  slash to home page.

* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.