build: Fix 'AM_V_at' typo.

* Makefile.am (hydra-jobs.scm): Fix 'AM_V_at' typo.

grafts: Rename files whose name matches a graft.

Fixes <http://bugs.gnu.org/23132>.
Reported by Mark H Weaver <mhw@netris.org>.

* guix/build/graft.scm (rename-matching-files): New procedure.
(rewrite-directory): Use it.
* tests/grafts.scm ("graft-derivation, renaming"): New test.

grafts: Preserve empty directories when grafting.

* guix/build/graft.scm (rewrite-directory)[rewrite-leaf]: Add case for
'directory.
Pass #:directories? #t to 'find-files'.

substitute: Gracefully handle invalid store file names.

Before, something like:

  echo have /gnu/foo | ./test-env guix substitute --query

would lead to an ugly backtrace.

* guix/scripts/substitute.scm (narinfo-cache-file): Call 'leave' when
'store-hash-part' returns #f.

graph: Allow store file names for 'derivation' and 'references' graphs.

* guix/scripts/graph.scm (%derivation-node-type)[convert]: Add
'derivation-path?' and catch-all clauses.
(%reference-node-type)[convert]: Add 'store-path?' and catch-all
clauses.
(assert-package, nodes-from-package): New procedures.
(%package-node-type, %bag-node-type,%bag-with-origins-node-type)
(%bag-emerged-node-type): Add 'convert' field
(guix-graph): Rename 'packages' to 'items' and
allow 'store-path?' arguments.
* guix/graph.scm (<node-type>)[convert]: Adjust comment.
* doc/guix.texi (Invoking guix graph): Document it.

derivations: 'derivation' sorts items in the resulting object.

* guix/derivations.scm (derivation-input<?): New procedure.
(write-derivation)[coalesce-duplicate-inputs]: Remove.
Remove calls to 'sort'.
(coalesce-duplicate-inputs): New procedure.
(derivation-hash): Sort INPUTS and use 'coalesce-duplicate-inputs'.
(derivation)[input->derivation-input]
[coalesce-duplicate-inputs]: New procedures.
Sort OUTPUTS, INPUTS, and ENV-VARS.
* tests/derivations.scm ("read-derivation vs. derivation"): New test.

graph: Use absolute file name canonicalization.

* guix/scripts/graph.scm (guix-graph): Wrap in 'with-fluids'.

gnu: linux-libre: Update to 4.5.5.

* gnu/packages/linux.scm (linux-libre): Update to 4.5.5.

gnu: linux-libre-4.4: Update to 4.4.11.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.11.

ant-build-system: Add unpack phase.

* guix/build/ant-build-system.scm (unpack): New procedure.
(%standard-phases): Use it.

gnu: Add default gcc-objc++.

* gnu/packages/gcc.scm (gcc-objc++): New variable.

gnu: Add gcc-objc++-4.9.

* gnu/packages/gcc.scm (gcc-objc++-4.9): New variable.

gnu: Add default gcc-objc.

* gnu/packages/gcc.scm (gcc-objc): New variable.

gnu: Add gcc-objc-4.9.

* gnu/packages/gcc.scm (gcc-objc-4.9): New variable.

gnu: r-rcpparmadillo: Update to 0.6.700.6.0.

* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.6.700.6.0.
* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to
6.700.6.

gnu: armadillo: Update to 6.700.7.

* gnu/packages/maths.scm (armadillo): Update to 6.700.7.

gnu: r-genomation: Update to 1.4.2.

* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.

gnu: r-jsonlite: Update to 0.9.20.

* gnu/packages/web.scm (r-jsonlite): Update to 0.9.20.

gnu: r-plotly: Update to 3.6.0.

* gnu/packages/statistics.scm (r-plotly): Update to 3.6.0.

gnu: r-matrixstats: Update to 0.50.2.

* gnu/packages/statistics.scm (r-matrixstats): Update to 0.50.2.