gnu: git: Update to 2.13.4.

* gnu/packages/version-control.scm (git): Update to 2.13.4.

gnu: r-foreign: Update hash after upstream tarball change.

* gnu/packages/statistics.scm (r-foreign):  Update hash.  The only difference
  in the tarball is the metadata.  The contents are identical.

gnu: r-foreign: Remove duplicate recipe.

* gnu/packages/statistics.scm (r-foreign): Remove duplicate recipe.

graph: Provide access to the package record in the emit functions.

* guix/graph.scm (export-graph): Pass the node to the emit functions, instead
  of the node's label.

guix package: Allow `guix package -u' to fuction as before.

This is a follow up to 6ddf97f81bb99a73f00e30ad5fc19577872b5b49

* guix/scripts/package.scm (%options) <"-u">: Only check for a flag when
there is an ARG after '-u'.

gnu: rapidjson: Update to 1.1.0.

* gnu/packages/web.scm (rapidjson): Update to 1.1.0.
[source]: Remove snippet.

gnu: Add pidentd.

* gnu/packages/networking.scm (pidentd): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: hyperrogue: Update to 10.0e.

* gnu/packages/games.scm (hyperrogue): Update to 10.0e.
[arguments]: Adjust accordingly.

gnu: metabat: Limit to x86_64 and i686 only.

* gnu/packages/bioinformatics.scm (metabat)[supported-systems]: New field.

gnu: Add emacs-yasnippet-snippets.

* gnu/packages/emacs.scm (emacs-yasnippet-snippets): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: emacs-yasnippet: Upgrade to 0.12.0.

* gnu/packages/emacs.scm (emacs-yasnippet): Upgrade to 0.12.0.
[source]: Remove an uninstalled directory from yas-snippet-dirs.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: guile-ssh: Update to 0.11.2.

* gnu/packages/ssh.scm (guile-ssh): Update to 0.11.2.
[source]: Remove 'patches', 'modules', and 'snippet'.
* gnu/packages/patches/guile-ssh-channel-finalization.patch,
gnu/packages/patches/guile-ssh-double-free.patch,
gnu/packages/patches/guile-ssh-rexec-bug.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Remove them.

gnu: artanis: Unbundled guile-json and version according to documentation.

* gnu/packages/guile.scm (artanis): Unbundled guile-json and version
according to documentation.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

lint: formatting: Detect sexp boundaries.

* guix/scripts/lint.scm (report-formatting-issues)[last-line]: Remove.
[sexp-last-line]: New procedure.
Use it.

gnu: python-pbr-minimal: Update to 3.0.1

* gnu/packages/python.scm (python-pbr-minimal): Update to 3.0.1
[source]: Update hash and remove patch.
* gnu/packages/patches/python-pbr-fix-man-page-support.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: libgit2: Enable SHA-1 collision detection.

* gnu/packages/version-control.scm (libgit2)[arguments]: Enable '-DUSE_SHA1DC'
in #:configure-flags.

gnu: ruby-bio-commandeer: Update to 0.2.0.

* gnu/packages/ruby.scm (ruby-bio-commandeer): Update to 0.2.0.

gnu: libmicrohttpd: Update to 0.9.55.

* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.55.
[arguments]: Add 'add-missing-LDFLAGS' phase.

guix package: Warn when invoked with '-u -something'.

Fixes <https://bugs.gnu.org/27820>.
Reported by Hartmut Goebel <h.goebel@crazy-compilers.com>.

* guix/scripts/package.scm (%options) <"-u">: Emit a warning when ARG
starts with "-".

gnu: xf86-video-intel: Update snapshot.

* gnu/packages/xorg.scm (xf86-video-intel): Update to 2100efa.
Introduce 'revision' variable.