* emacs.am ($(AUTOLOADS)): Write to $(builddir), not $(srcdir).

This allows substitute servers to tell 'guix substitute' how long they
can cache narinfo lookups.

* guix/scripts/substitute.scm (cache-narinfo!): Add 'ttl' parameter.
[cache-entry]: Honor it.
(fetch-narinfos)[handle-narinfo-response]: Check the 'Cache-Control'
header of RESPONSE and pass its 'max-age' value to 'cache-narinfo!'.

* guix/scripts/substitute.scm (cached-narinfo): Expect 'narinfo' sexp
version 2 with a 'ttl' field.
(cache-narinfo!)[cache-entry]: Produce 'narinfo' sexp version 2 with a
'ttl' field.
(remove-expired-cached-narinfos)[expired?]: Read 'narinfo' sexp version 2.

* gnu/packages/algebra.scm (cm): Update to 0.3.
  [license]: Change to gpl3+.

* config-daemon.ac: Check for (gnutls) and define 'GUIX_SUBSTITUTE_URLS'.
* nix/nix-daemon/guix-daemon.cc (main): Use GUIX_SUBSTITUTE_URLS.
* guix/store.scm (%default-substitute-urls): Use 'https' when (gnutls)
is available.
* doc/guix.texi (Binary Installation): Mention mirrors
(Invoking guix-daemon): Mention mirror.hydra.gnu.org.
(Substitutes): Mention mirrors.
(Invoking guix archive): Show https URLs.

* guix/http-client.scm (http-fetch): Do not call 'setvbuf' on non-file
ports.

* gnu/packages/bioinformatics.scm (r-dnacopy): New variable.

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

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

* gnu/packages/disk.scm (idle3-tools): New variable.

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

* gnu/packages/version-control.scm (neon): Update to 0.30.1.

* gnu/packages/version-control.scm (mercurial): Update to 3.7.2.
[source]: Update to mercurial-scm.org.
[home-page]: Same.

* gnu/packages/gtk.scm (gdk-pixbuf+svg): New variable.

* gnu/packages/version-control.scm (git): Update to 2.7.3.
(git-manpages)[source]: Update hash.

* gnu/services/desktop.scm (package-direct-input-selector): New
  function.
  (<gnome-desktop-configuration>, gnome-desktop-service-type)
  (<xfce-desktop-configuration>, xfce-desktop-service-type): New
  variables.
  (gnome-desktop-service, xfce-desktop-service): New public variables.

* doc/guix.texi (Desktop Services): Document new variables.

* gnu/packages/xfce.scm (xfce)[propagated-inputs]: Add xfce4-power-manager.

* gnu/packages/xfce.scm (xfce4-power-manager): New variable.

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

* gnu/packages/linux-libre-x86_64.conf: Rename to ...
* gnu/packages/linux-libre-4.4-x86_64.conf: ... this.
* gnu/packages/linux-libre-i686.conf: Rename to ...
* gnu/packages/linux-libre-4.4-i686.conf: ... this.
* gnu/packages/linux-libre-4.5-i686.conf,
gnu/packages/linux-libre-4.5-x86_64.conf: New files.
* Makefile.am (KCONFIGS): Update accordingly.
* gnu/packages/linux.scm (linux-libre): Update to 4.5.
(linux-libre-4.4): New variable.

* doc/guix.texi ("Using the Configuration System"): Move the example...
("Service Reference"): ...to here, and clarify more.
* gnu/services.scm (modify-services): Update docstring to mention the
return type.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

Suggested by Nils Gillmann <niasterisk@grrlz.net>.

* doc/guix.texi (Hardware Considerations): New node.
(operating-system Reference): Mention it.

* gnu/packages/version-control.scm (gitolite): Update to 3.6.5.
[source]: Remove patch.
* gnu/packages/patches/gitolite-openssh-6.8-compat.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.

* gnu/packages/version-control.scm (shflags): Update to 1.2.0.
[source]: Switch to github.
[home-page]: Project moved to github.

* gnu/packages/version-control.scm (libgit2): Update to 0.24.0.
[inputs]: Switch python to python-wrapper.

* guix/grafts.scm (references-oracle)[references*]: Add call to
'substitution-oracle'.

The connection used to fetch /nix-cache-info is now reused for the
subsequent narinfo requests.

* guix/scripts/substitute.scm (download-cache-info)[download]: Remove.
[uri, read-cache-info]: New variables.
Rewrite in terms of 'http-fetch' instead of 'fetch'.  Return an open
port in addition to a <cache-info>.
* guix/scripts/substitute.scm (http-multiple-get): Add #:port parameter
and honor it.
(fetch-narinfos)[do-fetch]: Add 'port' parameter.
Adjust to new 'download-cache-info' and 'do-fetch' signatures.

* guix/http-client.scm (http-fetch): Add #:keep-alive? parameter and
pass it to 'http-get' or 'http-get*'.

This parameter became unused with the switch to HTTP pipelining in
commit d3a65203.

* guix/scripts/substitute.scm (fetch): Remove #:quiet-404? and adjust
accordingly.

* guix/store.scm (%reference-cache): New variable.
(references/substitutes): Use it.

* guix/scripts/size.scm (guix-size): Parametrize '%graft?'.

This is a follow-up to commit 1068f26b.
Reported by Alex Kost <alezost@gmail.com>.

* doc/guix.texi (Building the Installation Image): Replace @xref by @ref.

* gnu/packages/kodi.scm (kodi): Update to 16.0.
[inputs]: Add crossguid, dcadec, and util-linux.

* gnu/packages/audio.scm (dcadec): New variable.

* gnu/packages/kodi.scm (crossguid): New variable.

* gnu/packages/bioinformatics.scm (htsjdk)[build-system]: Use
ant-build-system.
[arguments]: Adapt for ant-build-system.

* guix/build-system/ant.scm: New file.
* guix/build/ant-build-system: New file.
* Makefile.am (MODULES): Add new files.
* doc/guix.texi (Build Systems): Document ant-build-system.

* gnu/packages/java.scm (ant)[source]: Use Apache mirror instead of
  plain URL.

* guix/build/install.scm (reset-timestamps): Reset timestamps of
  directories as well.

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

* gnu/packages/enlightenment.scm (enlightenment): Update to 0.20.6.

* gnu/packages/mail.scm (khard): New variable.

* gnu/packages/python.scm (python-vobject, python2-vobject): New variables.