gnu: r-genomicfeatures: Update to 1.28.4.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.

gnu: r-copywriter: Update to 2.8.1.

* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.

gnu: r-sva: Update to 3.24.4.

* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.

gnu: r-rsqlite: Update to 2.0.

* gnu/packages/statistics.scm (r-rsqlite): Update to 2.0.

gnu: Add r-blob.

* gnu/packages/statistics.scm (r-blob): New variable.

gnu: Add r-pkgconfig.

* gnu/packages/statistics.scm (r-pkgconfig): New variable.

pull: Honor '--no-grafts'.

* guix/scripts/pull.scm (guix-pull): Parameterize %GRAFT? as a function
of OPTS.

pull: Use the commit ID as the version string.

* guix/scripts/pull.scm (build-from-source): Add #:commit parameter.
Pass it to BUILD.
(build-and-install): Add #:commit and pass it to 'build-from-source'.
(guix-pull): Pass #:commit to 'build-and-install'.

pull: Fetch source code from Git.

* guix/scripts/pull.scm (%snapshot-url, with-environment-variable)
(with-PATH): Remove.
(ensure-guile-git!): New procedure.
(%repository-url): New variable.
(%default-options): Add 'repository-url' and 'ref'.
(show-help, %options): Add '--commit' and '--url'.
(temporary-directory, first-directory, interned-then-deleted)
(unpack): Remove.
(build-from-source): Rename 'tarball' to 'source'.  Remove call to
'unpack'.
(build-and-install): Rename 'tarball' to 'source'.
(honor-lets-encrypt-certificates!, report-git-error): New procedures.
(with-git-error-handling): New macro.
(guix-pull)[fetch-tarball]: Remove.
Wrap body in 'with-git-error-handling'.  Rewrite to use
'latest-repository-commit'.
* build-aux/build-self.scm (build): Print an error message and exit when
GUILE-GIT is #f.
* doc/guix.texi (Invoking guix pull): Mention Git.  Document '--commit'
and '--branch'.

build: Make Guile-Git a hard requirement.

* configure.ac: Error out when (git) is missing.
* doc/guix.texi (Requirements): Mention Guile-Git.
* Makefile.am (MODULES): Add guix/git.scm unconditionally.

gnu: re2: Update to 2017-08-01.

* gnu/packages/regex.scm (re2): Update to 2017-08-01.

gnu: maim: Update to 5.4.66.

* gnu/packages/xdisorg.scm (maim): Update to 5.4.66.

gnu: slop: Update to 7.3.48.

* gnu/packages/xdisorg.scm (slop): Update to 7.3.48.

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>