Now that the build system does wrapping automatically, it can be removed from
the packages that do it manually.

* gnu/packages/databases.scm (es-dump-restore)[arguments]: Remove #:phases.
* gnu/packages/ruby.scm (ruby-redcloth)[arguments]: Remove #:phases.
  (ruby-httpclient)[arguments]: Remove 'wrap-bin-httpclient from the modified
  phases.

Wrap files in bin/ and sbin/ with the location of the gem itself and the
location of any other gems in use (GEM_PATH). This ensures that the bin files
will run with the right environment when executed.

It does however mean that native-inputs will also get wrapped up in any
binaries, which is not good, as it increases the size of the closure, and
risks this code being used at runtime.

* guix/build/ruby-build-system.scm (wrap): New procedure.
  (%standard-phases): Add the wrap phase.

A modified copy of wrap-program from (guix build utils). The wrap-program
procedure doesn't work well for Ruby scripts, as it breaks using the -S flag
with ruby to execute the script, as when -S is passed to ruby, it expects the
script on the PATH to use ruby in the shebang, and not bash.

Therefore, to wrap the program, but keep the shebang as ruby, wrap it with a
ruby script instead.

wrap-ruby-program uses .real/foo rather than .foo-real, as this might be
neater. This procedure also includes a call to Gem.clear_paths to make it
possible to set the GEM_PATH through this method, and for it to take effect.

* gnu/build/ruby-build-system.scm (wrap-ruby-program): New procedure.

* guix/build/ruby-build-system.scm (install): Install gems to the vendor
  directory, rather than the GEM_HOME. The vendor directory does not include
  the version of ruby used to install the gem in the path, which makes it
  easier to add it to the GEM_PATH for all versions of ruby to use.
  (gem-home): Remove procedure.
* gnu/packages/ruby.scm (ruby, ruby-2.1)[native-search-paths]: Switch to
  lib/ruby/vendor_ruby.
  (ruby-1.8)[native-search-paths]: Remove native-search-paths.
  (gem-directory): Remove procedure.
  (ruby-ansi, ruby-ae)[arguments]: Remove use of gem-directory.
  (ruby-metaclass, ruby-instantiator, ruby-introspection, ruby-mocha,
  ruby-nokogiri, ruby-minitest-tu-shim, ruby-redcloth)[arguments]: Remove use
  of gem-home.
  (ruby-git, ruby-httpclient)[arguments]: Remove use of GEM_HOME.
* gnu/packages/databases.scm (es-dump-restore)[arguments]: Remove use of
  GEM_HOME.

* gnu/packages/algebra.scm (arb): Update to 2.12.0.

* gnu/packages/algebra.scm (pari-gp): Update to 2.9.4.

* doc/guix.texi (Web Services): The body of an NGINX-LOCATION-CONFIGURATION
is a list of strings and not a string.

OpenSSL and zlib are referred to by the built package, so we make them
regular inputs.

This is a followup to commit e8b40974.

* gnu/packages/cpp.scm (rct)[native-inputs]: Move openssl and zlib to ...
[inputs]: ... new field.

* gnu/packages/cpp.scm (rct): New variable.

* gnu/packages/flashing-tools.scm (flashrom): Update to 1.0.

* gnu/packages/flashing-tools.scm (flashrom)[home-page]: Use HTTPS.

This follows up commit 7641266b.

* gnu/packages/mpd.scm: Don't #:use-module (gnu packages gcc).

* gnu/packages/mpd.scm (libmpdclient, mpd, mpd-mpc, ncmpc)[home-page]: Use
HTTPS.

* gnu/packages/mpd.scm (mpdscribble)[home-page]: This package seems to have
found a home.  Use it.

* gnu/packages/mpd.scm (libmpdclient): Update to 2.13.
[build-system]: Switch to meson-build-system.
[native-inputs]: Add pkg-config and check.
[arguments]: Enable tests and build documentation.

* gnu/packages/pcre.scm (pcre, pcre2)[home-page]: Use HTTPS.

* gnu/packages/audio.scm (gsm): Update to 1.0.17.

* gnu/packages/video.scm (youtube-dl): Update to 2018.01.14.

* gnu/packages/admin.scm (libcap-ng)[home-page]: Use HTTPS.

* gnu/packages/compression.scm (lz4): Update to 1.8.1.
[arguments]: Enable ‘#:parallel-tests?’, now considered safe upstream.
Use ‘more GNU’-style lowercase ‘prefix=’.

* gnu/packages/kde.scm (krita): Update to 3.3.3.

* gnu/packages/xfce.scm (gtk-xfce-engine, libxfce4util, xfconf, libxfce4ui)
(exo, garcon, tumbler, xfce4-panel, xfce4-battery-plugin)
(xfce4-clipman-plugin, xfce4-pulseaudio-plugin, xfce4-xkb-plugin)
(xfce4-appfinder, xfce4-session, xfce4-settings, thunar, thunar-volman)
(xfwm4, xfdesktop, xfce4-terminal, xfce, xfce4-power-manager, ristretto)
(xfce4-taskmanager, orage)[home-page]: Use HTTPS.

* gnu/packages/xfce.scm (xfce4-terminal): Update to 0.8.6.

* gnu/packages/gl.scm (gl2ps): Update to 1.4.0.

* gnu/packages/admin.scm (dmidecode): Update to 3.1.

* gnu/packages/gnupg.scm (gpgme): Update to 1.10.0.
[arguments]: Remove ‘patch-cmake-file’ work-around for fixed bug.

* gnu/packages/mail.scm (offlineimap): Update to 7.1.5.

* gnu/packages/code.scm (lcov): Update to 1.13.
[arguments]: Remove superfluous #:make-flags.

* gnu/packages/java.scm (java-powermock-modules-junit4)[arguments]: Fix
junit version detection.

* gnu/packages/java.scm (java-powermock-core)[arguments]: Add a phase to
include resources.

* gnu/packages/package-management.scm (guix): Update to 0dcf675c.

Fixes a regression introduced in
d4d7d709 which broke
'hunspell-dict-en' (but not the 'hunspell-dict-en-*' variants.)

* gnu/packages/aspell.scm (aspell-word-list)[install]: Check whether
'LANGUAGE.dic' exist before installing it.  If it doesn't exist, install
all of *.dic.

This mostly reverts 17af5d51.
Suggested by Andy Wingo <wingo@igalia.com>.

* guix/ssh.scm (remote-daemon-channel)[redirect]: Remove 'read!' FFI
hack.  Use buffered ports.

Fixes <https://bugs.gnu.org/26008>.
Reported by Myles English <mylesenglish@gmail.com>.

* guix/ssh.scm (retrieve-files*): Move error reporting to...
(report-guile-error, report-module-error): ... here.  New procedures.
* guix/scripts/offload.scm (assert-node-repl): Use 'report-guile-error'.
(assert-node-has-guix): Explicitly check for 'use-modules' first.  Use
'report-module-error'.

Fixes <https://bugs.gnu.org/28057>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* guix/scripts/offload.scm (assert-node-has-guix): Catch
'node-repl-error' and call 'leave'.

* guix/ssh.scm (retrieve-files): Remove the subset of FILES that is
valid in LOCAL.
(store-export-channel): Add comment.

This fixes a regression in 'retrieve-files*' introduced in
896fec47, whereby (guix scripts offload)
would not read the initial sexp now sent by the remote host via
'store-export-channel'.  This would effectively prevent file retrieval
entirely when offloading.

* guix/ssh.scm (retrieve-files*): New procedure, like former
'retrieve-files' but with an extra #:import parameter.
(retrieve-files): Rewrite in terms of 'retrieve-files*'.
(file-retrieval-port): Make private.
* guix/scripts/offload.scm (transfer-and-offload): Pass #:import to
'retrieve-files*'.
(retrieve-files*): Remove.

* gnu/packages/patches/transmission-fix-dns-rebinding-vuln.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bittorrent.scm (transmission)[source]: Use it.

* gnu/packages/bootloaders.scm (dtc): Update to 1.4.6.
[source]: Remove both patches.
* gnu/packages/patches/dtc-format-modifier.patch: Delete file.
* gnu/packages/patches/dtc-32-bits-check.patch: Likewise.
* gnu/local.mk (dist_patch_DATA): Remove both.

* gnu/packages/engineering.scm (harminv): Update to 1.4.1.
[source, home-page]: Switch to new host.