Fixes <https://bugs.gnu.org/36371>.
Reported by Tobias Geerinckx-Rice <me@tobias.gr>.

* guix/git.scm (git-checkout-compiler): Pass 'tag-or-commit' to
'latest-repository-commit*'.
* doc/guix.texi (Package Transformation Options): Update '--with-commit'
documentation accordingly.
* tests/guix-build-branch.sh: Add test.

* guix/git.scm (switch-to-ref)[obj]: Wrap in 'resolve' lambda.  Add
'tag-or-commit' case.
(update-cached-checkout): Document it.

* gnu/packages/telephony.scm (jami-client-gnome): Rename to...
(jami): ... this.  Update 'name' field accordingly.
(jami-client-gnome): New variable.

* gnu/packages/video.scm (vlc): Update to 3.0.7.1.

* gnu/packages/admin.scm (clusterssh)[arguments]:
Add ’augment-library-path’ phase so libraries are found.
[propagated-inputs]: Make all of these…
[inputs]: …regular.

* gnu/packages/video.scm (youtube-dl): Update to 2019.07.16.

* gnu/packages/mail.scm (dkimproxy)[arguments]: Wrap dkim_responder.pl.
[inputs]: Add perl-mime-tools and perl-timedate.

This is a follow-up to 66e39000, in a
way, since it adds the forgotten *6 inputs.

* gnu/packages/mail.scm (dkimproxy)[arguments]: Refactor ’make-wrapper’ phase.
Add perl-io-socket-inet6 and perl-socket6 to the list.

* gnu/packages/mail.scm (dkimproxy)[synopsis]: Do so.
[description]: Also.

* gnu/packages/networking.scm (perl-net-dns-resolver-mock)[synopsis]:
Remove unfortunate ‘a’.
[description]: Fix typo.  Edit for clarity.

* gnu/packages/networking.scm (perl-net-dns-resolver-mock)[inputs]:
Move perl-net-dns to here…
[propagated-inputs]: …from here.

* gnu/packages/mail.scm (dkimproxy)[license]: Change to gpl2+.

* gnu/packages/mail.scm (dkimproxy)[source]: Add patch.
* gnu/packages/patches/dkimproxy-add-ipv6-support.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Should fix <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36634>.

* gnu/packages/virtualization.scm (libvirt)[source]: Add patch.
* gnu/packages/patches/libvirt-remove-ATTRIBUTE_UNUSED.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

* gnu/packages/admin.scm (clusterssh)[arguments]: Add ‘refer-to-inputs’ and ‘delete-failing-tests’ phases.
[inputs]: Move xterm to here…
[propagated-inputs]: …from here.

* gnu/packages/admin.scm (clusterssh)[propagated-inputs]:
Add perl-sort-naturally.

* gnu/packages/mail.scm (dkimproxy): New variable.

* gnu/packages/mail.scm (perl-mail-dkim): New variable.

* gnu/packages/networking.scm (perl-net-dns-resolver-mock): New
variable.

* gnu/packages/mail.scm (perl-mail-authenticationresults): New variable.

*  gnu/packages/golang.scm (go-1.12): Update to 1.12.7.

* gnu/packages/golang.scm (go-1.11): Update to 1.11.12.

* gnu/packages/mail.scm (exim): Update to 4.92.1.

* gnu/packages/xorg.scm (xpra): Update to 2.5.3.

* gnu/packages/ebook.scm (xchm): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/games.scm (starfighter): Update to 2.0.0.3.
[source]: Use url-fetch and remove 'file-name' field.
[native-inputs]: Remove autoconf and automake.

* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change
'guile-json' to 'guile-json-1'.
* gnu/packages/ci.scm (cuirass)[inputs]: Likewise.
* gnu/packages/guile-xyz.scm (artanis)[inputs]: Likewise.
* gnu/packages/guile-xyz.scm (jupyter-guile-kernel)[inputs]: Likewise.
* gnu/packages/guile-xyz.scm (guile-mastodon)[inputs]: Likewise.
* gnu/packages/mail.scm (mumi)[inputs]: Likewise.
* gnu/packages/package-management.scm (guix)[inputs]: Likewise.
* gnu/packages/package-management.scm (guix-daemon)[inputs]: Likewise.
* gnu/packages/web.scm (hpcguix-web)[inputs]: Likewise.

* gnu/packages/guile.scm (guile-json-1): New variable.

Guile-JSON 3.x is incompatible with Guile-JSON 1.x, which we relied on
until now: it maps JSON dictionaries to alists (instead of hash tables),
and JSON arrays to vectors (instead of lists).  This commit is about
adjusting all the existing code to this new mapping.

* m4/guix.m4 (GUIX_CHECK_GUILE_JSON): New macro.
* configure.ac: Use it.
* doc/guix.texi (Requirements): Mention the Guile-JSON version.
* guix/git-download.scm (git-fetch)[guile-json]: Use GUILE-JSON-3.
* guix/import/cpan.scm (string->license): Expect vectors instead of
lists.
(module->dist-name): Use 'json-fetch' instead of 'json-fetch-alist'.
(cpan-fetch): Likewise.
* guix/import/crate.scm (crate-fetch): Likewise, and call 'vector->list'
for DEPS.
* guix/import/gem.scm (rubygems-fetch): Likewise.
* guix/import/json.scm (json-fetch-alist): Remove.
* guix/import/pypi.scm (pypi-fetch): Use 'json-fetch' instead of
'json-fetch-alist'.
(latest-source-release, latest-wheel-release): Call 'vector->list' on
RELEASES.
* guix/import/stackage.scm (stackage-lts-info-fetch): Use 'json-fetch'
instead of 'json-fetch-alist'.
(lts-package-version): Use 'vector->list'.
* guix/import/utils.scm (hash-table->alist): Remove.
(alist->package): Pass 'vector->list' on the inputs fields, and default
to the empty vector.
* guix/scripts/import/json.scm (guix-import-json): Remove call to
'hash-table->alist'.
* guix/swh.scm (define-json-reader): Expect pair? or null? instead of
hash-table?.
[extract-field]: Use 'assoc-ref' instead of 'hash-ref'.
(json->branches): Use 'map' instead of 'hash-map->list'.
(json->checksums): Likewise.
(json->directory-entries, origin-visits): Call 'vector->list' on the
result of 'json->scm'.
* tests/import-utils.scm ("alist->package with dependencies"): New test.
* gnu/installer.scm (build-compiled-file)[builder]: Use GUILE-JSON-3.
* gnu/installer.scm (installer-program)[installer-builder]: Likewise.
* gnu/installer/locale.scm (iso639->iso639-languages): Use 'assoc-ref'
instead of 'hash-ref', and pass vectors through 'vector->list'.
(iso3166->iso3166-territories): Likewise.
* gnu/system/vm.scm (system-docker-image)[build]: Use GUILE-JSON-3.
* guix/docker.scm (manifest, config): Adjust for Guile-JSON 3.
* guix/scripts/pack.scm (docker-image)[build]: Use GUILE-JSON-3.
* guix/import/github.scm (fetch-releases-or-tags): Update docstring.
(latest-released-version): Use 'assoc-ref' instead of 'hash-ref'.  Pass
the result of 'fetch-releases-or-tags' to 'vector->list'.
* guix/import/launchpad.scm (latest-released-version): Likewise.

* gnu/packages/bioconductor.scm (r-depecher): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/bioconductor.scm (r-mixomics): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/bioconductor.scm (r-flowsom): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/bioconductor.scm (r-flowmeans): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/bioconductor.scm (r-consensusclusterplus): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/bioconductor.scm (r-flowutils): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/bioconductor.scm (r-flowcore): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/bioconductor.scm (r-all): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/cran.scm (r-kableextra): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/cran.scm (r-umap): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/emacs-xyz.scm (emacs-gitpatch): Update to 0.5.1.