doc: Clarify and consolidate modify-services documentation.

* 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>

doc: Add "Hardware Considerations" node.

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

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

gnu: gitolite: Update to 3.6.5.

* 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: shflags: Update to 1.2.0.

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

gnu: libgit2: Update to 0.24.0.

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

grafts: Update the narinfo cache before building a derivation.

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

substitute: Keep the initial connection alive.

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.

http-client: Add #:keep-alive? parameter.

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

substitute: Remove dead code.

This parameter became unused with the switch to HTTP pipelining in
commit d3a652037ef879f9279bc056c43d15ba7afcbb25.

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

store: 'references/substitutes' caches its results.

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

size: Disable grafts.

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

doc: Fix incorrect use of @xref.

This is a follow-up to commit 1068f26b797ed7c1475d93cab6eed53c9097c7f6.
Reported by Alex Kost <alezost@gmail.com>.

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

gnu: kodi: Update to 16.0.

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

gnu: Add dcadec.

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

gnu: Add crossguid.

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

gnu: htsjdk: Use ant-build-system.

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

build: Add 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: ant: Update source URL.

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

build: reset-timestamps: Include directories.

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

gnu: Add pyicoteo.

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