* guix/packages.scm (package-input-rewriting): Add #:deep? and pass it
to 'package-mapping'.
[replacement-property]: New variable.
[rewrite]: Check it.
[cut?]: New procedure.
* tests/packages.scm ("package-input-rewriting"): Pass #:deep? #f and
ensure implicit inputs were not rewritten.  Avoid 'eq?' comparisons.
("package-input-rewriting, deep"): New test.
* gnu/packages/guile.scm (package-for-guile-2.0, package-for-guile-3.0):
Pass #:deep? #f.

Previously, something like:

  guix build glib --with-graft=glibc=glibc@2.29

would produce a result showing that rewriting rules were not applied to
libx11@1.6.A (a replacement).

* guix/packages.scm (package-mapping): Call REPLACE instead of PROC to
'replacement'.
* tests/packages.scm ("package-input-rewriting/spec, graft"): New test.

With this change, '--with-input', '--with-graft', etc. also apply to
implicit dependencies.  Thus, it's now possible to do:

  guix build python-itsdangerous --with-input=python-wrapper=python@2

or:

  guix build hello --with-graft=glibc=glibc@2.29

Additionally, before, implicit inputs were not rewritten, which could
lead to duplicates in the output of 'bag-transitive-inputs' (packages
that are not 'eq?' but lead to the same derivation).  This in turn would
lead to unnecessary rebuilds when using '--with-input' & co.  This
change fixes it by ensuring even implicit inputs are rewritten.

Fixes <https://bugs.gnu.org/42156>.

* guix/packages.scm (package-input-rewriting/spec): Add #:deep?
defaulting to #true, and pass it to 'package-mapping'.
[replacement-property]: New variable.
[rewrite]: Check that property and set it on the result of PROC.
[cut?]: New procedure.
* tests/packages.scm ("package-input-rewriting/spec"): Ensure implicit
inputs were unchanged.
("package-input-rewriting/spec, partial match"): Pass #:deep? #f.
("package-input-rewriting/spec, deep")
("package-input-rewriting/spec, no duplicates"): New tests.
(package/inherit): Move before use.
* tests/guix-build.sh: Add tests.
* tests/scripts-build.scm ("options->transformation, with-graft"):
Compare dependencies by package name or derivation file name.
* doc/guix.texi (Defining Packages): Adjust accordingly.

* guix/packages.scm (build-system-with-package-mapping): New procedure.
(package-mapping): Add #:deep? and honor it.
* tests/packages.scm ("package-mapping"): Compare the direct inputs of
the bag of P0 and that of P1.
("package-mapping, deep"): New test.

* guix/scripts/build.scm (transform-package-tests): New procedure.
(%transformations, %transformation-options)
show-transformation-options-help): Add it.
* tests/scripts-build.scm ("options->transformation, without-tests"):
New test.
* doc/guix.texi (Package Transformation Options): Document it.

* gnu/packages/linux.scm (bbswitch-module): Update to 20200526.

* gnu/packages/emacs-xyz.scm (emacs-mood-line)[license]: Switch to GPL2+.

* gnu/packages/emacs-xyz.scm (emacs-mood-line): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

* doc/guix.texi (Bootloader Configuration)[bootloader]: Add
grub-efi-netboot-bootloader.
[target]: Document TFTP root directory for grub-efi-netboot-bootloader.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

* gnu/bootloader/grub.scm (grub-efi-netboot-bootloader): New variable.
(install-grub-efi-netboot): New procedure.
(grub-root-search): Update comment.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

* gnu/packages/gps.scm (gama): Update to 2.10.

* gnu/packages/ebook.scm (cozy): Update to 0.7.1.
[arguments]: Substitute only the Exec line in the desktop file.

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

* gnu/packages/compression.scm (lzlib)[arguments]: Pass "--disable-static".

Until now, since lzlib's 'configure' ignores '--host', we'd always end
up building it natively.

* gnu/packages/compression.scm (lzlib)[arguments]: Use (cc-for-target)
instead of "gcc".

* gnu/packages/linux.scm (ipset): New variable.

* gnu/packages/ssh.scm (webssh): New variable.

* gnu/packages/statistics.scm (emacs-ess): Update to 18.10.2-0.24da603.
[version]: Use version-revision-commit for version numbering.
[source]: Fix snippet for removing julia-mode.  Remove snippet to modify
roxy-preview-Rd-test.  Add snippet to modify r-help-mode test.  Add
snippet to fix install target to install files to correct directories.
Correct Makefile so that ess-autoloads.el is not built twice.
[arguments]: Add flag to specify INFODIR.  Remove patch modifying SHELL.
[license]: License is now GPLv3+.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

* gnu/packages/emacs-xyz.scm (emacs-auctex): Update to 12.2.5.

* gnu/packages/emacs-xyz.scm (emacs-edit-indirect): Update to 0.1.6.

* gnu/packages/emacs-xyz.scm (emacs-edit-indirect): Fix license field.

* doc/guix.texi (Transparent Emulation with QEMU): Use @var instead of
angle brackets for meta-syntactic variables.

Reported by Andreas Enge.

* doc/guix.texi (Transparent Emulation with QEMU): Remove "--hda" in
'image' example.

* doc/guix.texi (The Hurd in a Virtual Machine): Add instructions for
VNC and SSH access.  Mention childhurd secrets and /etc/childhurd.

* gnu/packages/mes.scm (nyacc): Rename to...
(nyacc-0.99): ... this.
(nyacc): New variable.
(mes)[propagated-inputs]: Replace NYACC with NYACC-0.99.
(mes-rb5)[native-inputs]: Likewise.
* gnu/packages/commencement.scm (mes-boot)[native-inputs]: Likewise.
(tcc-boot0)[native-inputs]: Likewise.

* gnu/packages/rust.scm (rust-1.20)[arguments]: Replace hardcoded x86_64
triplet with nix-system->gnu-triplet-for-rust in 'delete-install-logs phase.

* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.237.
(linux-libre-4.4-pristine-source): Update hash.

* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.237.
(linux-libre-4.9-pristine-source): Update hash.

* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.199.
(linux-libre-4.14-pristine-source): Update hash.

* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.147.
(linux-libre-4.19-pristine-source): Update hash.

* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.67.
(linux-libre-5.4-pristine-source): Update hash.

* gnu/packages/linux.scm (linux-libre-5.8-version): Update to 5.8.11.
(linux-libre-5.8-pristine-source): Update hash.

* gnu/packages/package-management.scm (guix)[propagated-inputs]: Use
GNUTLS instead of GUILE3.0-GNUTLS.
(guix-daemon)[inputs]: Likewise.
* guix/self.scm (specification->package): Likewise.

* gnu/packages/games.scm: (freedink-engine): Make public.
[arguments]: Add 'delete-freedinkedit-desktop' phase.
(freedink-data): Make public.

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

* gnu/packages/fonts.scm (font-adobe-source-serif-pro): Update to 3.001R.

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

* gnu/packages/fonts.scm (font-adobe-source-sans-pro): Update to 3.028R.

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

* guix/scripts/package.scm (package->manifest-entry*): Rewrite in terms
of 'manifest-entry-with-provenance'.

* gnu/ci.scm (hydra-jobs): Remove restriction for system to
equal (%current-system).

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/vim.scm (vim): Update to 8.2.1738.

* gnu/packages/ibus.scm (librime): Update to 1.6.1.
[inputs]: Add capnproto.
[native-inputs]: Add pkg-config.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

* gnu/packages/gnome.scm (komikku): Update to 0.21.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>