gnu: Add python-jmespath.

* gnu/packages/python.scm (python-jmespath): New variable.

gnu: Add python-tox.

* gnu/packages/python.scm (python-tox): New variable.

gnu: Add python-pluggy.

* gnu/packages/python.scm (python-pluggy): New variable.

gnu: Add python-rsa.

* gnu/packages/python.scm (python-rsa, python2-rsa): New variables.

gnu: Add python-colorama.

* gnu/packages/python.scm (python-colorama, python2-colorama): New
  variables.

gnu: Update sortmerna to 2.1.

* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.

gnu: ntp: Update to 4.2.8p6.

Fixes CVE-2015-{7973, 7974, 7975, 7976, 7977, 7978, 7979, 8138, 8158}.

* gnu/packages/ntp.scm (ntp): Update to 4.2.8p6.

gnu: Add linux-libre-4.1.

* gnu/packages/linux-libre-4.1-i686.conf,
  gnu/packages/linux-libre-4.1-x86_64.conf: New files.
* Makefile.am (KCONFIGS): Add them.
* gnu/packages/linux.scm (linux-libre-4.1): New variable.

gnu: linux-libre: Generalize 'kernel-config' to support variants.

* gnu/packages/linux.scm (kernel-config): Rewrite to support optional
  #:variant keyword argument.

gnu: linux-libre: Update to 4.4.1.

* gnu/packages/patches/linux-libre-CVE-2016-0728.patch: Delete file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/linux.scm (linux-libre): Update to 4.4.1.
  [source]: Remove patch.

gnu: Update socat to 1.7.3.1.

* gnu/packages/networking.scm (socat): Update to 1.7.3.1.

gnu: keepassx: Update to 2.0.1.

* gnu/packages/password-utils.scm (keepassx): Update to 2.0.1.

gnu: ccache: Update to 3.2.4.

* gnu/packages/ccache.scm (ccache): Update to 3.2.4.

emacs: command: Disambiguate "w" key in build options.

This is a followup to commit 47c0f92c37dc7d50d9d4598ce5b91c4cdfec6ed1.

* emacs/guix-command.el (guix-command-improve-common-build-argument):
  Use "W" key for '--with-input' option (leave "w" for '--with-source').

guix build: Add '--with-input'.

* guix/scripts/build.scm (transform-package-inputs): New procedure.
(%transformations): Add it.
(%transformation-options, show-transformation-options-help): Add
--with-input.
* tests/scripts-build.scm ("options->transformation, with-input"):
("options->transformation, with-input, no matches"): New tests.
* tests/guix-build.sh: Add tests.
* doc/guix.texi (Package Transformation Options): Document it.

build-system/python: Use 'ensure-keyword-arguments'.

* guix/build-system/python.scm (package-with-explicit-python): Use
'ensure-keyword-arguments'.

build: Remove semicolons from Guile warnings.

* build-aux/compile-all.scm (compile-file*):
Clear *CURRENT-WARNING-PREFIX*.

build: Really enable Guile warnings.

* build-aux/compile-all.scm (compile-options): Rename to...
(warnings): ... this.  Add 'unsupported-warning'.
(compile-file*): Pass '(#:warnings ...) as #:opts.

guix package: Support package transformation options.

* guix/scripts/package.scm (show-help): Call
'show-transformation-options-help'.
(%options): Append %TRANSFORMATION-OPTIONS.
(process-actions)[transform, transform-entry]: New procedures.
* doc/guix.texi (Invoking guix package): Mention package
transformations.
(Package Transformation Options): Mention 'guix package'.

guix build: Separate transformation options.

* guix/scripts/build.scm (%transformation-options): New variable.
(show-transformation-options-help): New procedure.
(show-help): Remove '--with-source' documentation and add
'show-transformation-options-help' call.
(%options): Remove "with-source" and append %TRANSFORMATION-OPTIONS.
* doc/guix.texi (Package Transformation Options): New node.  Document
'--with-source', moved from...
(Additional Build Options): ... here.