Use (ice-9 binary-ports) instead of (rnrs io ports).

This reduces the closure of (guix ui) from 123 to 106 modules.

* guix/derivations.scm: Use (ice-9 binary-ports) instead of (rnrs io
ports).
(map-derivation)[substitute-file]: Use 'read-string' instead of
'get-string-all'.
* guix/ftp-client.scm: Likewise.
* guix/hash.scm: Likewise.
* guix/http-client.scm: Likewise.
* guix/pki.scm (ensure-acl, current-acl): Likewise.
* guix/scripts/archive.scm (authorize-key)[read-key]: Likewise.
* guix/scripts/authenticate.scm (read-canonical-sexp)
(read-hash-data): Likewise.
* guix/scripts/download.scm: Likewise.
* guix/scripts/offload.scm (register-gc-root, remove-gc-roots)
(send-files): Likewise.
* guix/scripts/publish.scm (lazy-read-file-sexp): Likewise.
* guix/scripts/refresh.scm: Likewise.
* guix/scripts/substitute.scm (check-acl-initialized): Likewise.
* guix/serialization.scm (read-maybe-utf8-string): Likewise.
* guix/scripts/hash.scm (guix-hash): Use 'force-output' instead of
'flush-output-port'.
* guix/store.scm (process-stderr): Likewise.
* guix/tests.scm: Likewise.
* guix/utils.scm: Use (ice-9 binary-ports) and autoload (rnrs io ports)
for 'make-custom-binary-input-port'.

lint: Suggest @code instead of quotes.

* guix/scripts/lint.scm (%quoted-identifier-rx): New variable.
(check-description-style)[check-quotes]: New procedure.
Use it.
* tests/lint.scm ("description: suggest ornament instead of quotes"):
New test.

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

* guix/scripts/build.scm (transform-package-inputs/graft): New procedure.
(%transformations): Add 'with-graft'.
(%transformation-options): Likewise.
(show-transformation-options-help): Document it.
* tests/scripts-build.scm ("options->transformation, with-graft"): New
test.
* doc/guix.texi (Package Transformation Options): Document it.

guix build: Factorize transformation option parsing.

* guix/scripts/build.scm (%transformation-options): Introduce 'parser'
procedure and use it.

guix build: Extract '--with-input' replacement spec parsing.

* guix/scripts/build.scm (evaluate-replacement-specs): New procedure.
(transform-package-inputs)[not-equal]: Remove.
[replacements]: Define in terms of 'evaluate-replacement-specs'.

graph: Add '%referrer-node-type'.

* guix/scripts/graph.scm (ensure-store-items): New procedure.
(%reference-node-type)[convert]: Use it.
(non-derivation-referrers): New procedure.
(%referrer-node-type): New variable.
(%node-types): Add it.
* tests/graph.scm ("referrer DAG"): New test.
* doc/guix.texi (Invoking guix graph): Document it.

substitute: Make download messages more concise.

'guix substitute' now displays 2 lines per download instead of 4.
Suggested by Ricardo Wurmus.

* guix/scripts/substitute.scm (assert-valid-narinfo): Have #:verbose?
default to #f.  Remove leading newline in message.
(process-substitution): Display the URI rather than the store file name.
Display two newlines after the substitution.

guix system: Return two values when failing to talk to shepherd.

Before that, when 'guix system reconfigure' failed to talk to shepherd
and a 'system-error' was raised, we would get a "too few values returned
to continuation" error, which would prevent GRUB from being installed.

Reported by fps on #guix.

* guix/scripts/system.scm (warn-on-system-error): Remove.
(with-shepherd-error-handling): Inline former 'warn-on-system-error'.
Return two values when 'system-error' is raised.

lint: 'cve' checker reports the replacement's vulnerabilities.

Before, 'guix lint -c cve' would report the vulnerabilities of the
original package while pretending they are the vulnerabilities of the
replacement.

* guix/scripts/lint.scm (check-vulnerabilities): Consider the package
replacement before calling 'package-vulnerabilities'.
* tests/lint.scm ("cve: vulnerability fixed in replacement version"):
New test.

guix build: Gracefully handle packages without source for '-S'.

Fixes <http://bugs.gnu.org/22836>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* guix/scripts/build.scm (options->derivations): Gracefully
handle (package-source p) = #f.

system: grub.cfg uses correct file names when store is not in root partition.

Fixes <http://bugs.gnu.org/24346>.
Reported by csanchezdll@gmail.com (Carlos Sánchez de La Lama).

* guix/scripts/system.scm (previous-grub-entries): Get the initrd file
name from PARAMS.
* gnu/system.scm (operating-system-grub.cfg): Use
'operating-system-initrd-file' to retrieve the initrd file name.
* gnu/system/grub.scm (strip-mount-point): New procedure.
(grub-configuration-file)[entry->gexp]: Call 'strip-mount-point' for
LINUX and INITRD.

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

ui: Do not shadow '_' where it's used as a literal syntax match.

Fixes compilation with Guile 2.1.
Reported by Mu Lei.

* guix/ui.scm (report-load-error)
(warn-about-load-error, read/eval-package-expression): Use 'rest'
instead of '_' as the pattern variable name.
* gnu/packages.scm (%find-package): Likewise.
* guix/scripts/build.scm (transform-package-inputs): Likewise.
* guix/scripts/hash.scm (guix-hash): Likewise.
* guix/scripts/import/gnu.scm (%options, guix-import-gnu): Likewise.
* guix/scripts/import/nix.scm (guix-import-nix): Likewise.
* guix/scripts/offload.scm (build-machines): Likewise.
* guix/scripts/refresh.scm (%options): Likewise.
* guix/scripts/substitute.scm (narinfo-signature->canonical-sexp):
Likewise.

guix hash: Add --exclude-vcs option.

* guix/scripts/hash.scm (show-help): Add help text for --exclude-vcs option.
(%options): Add --exclude-vcs option.
(guix-hash): Handle exclude-vcs option.
* doc/guix.texi ("Invoking guix hash"): Update doc.
* tests/guix-hash.sh: Add test.

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

packages: Add 'package-superseded' and associated support.

This provides a way to mark a package as superseded by another one.
Upgrades replace superseded packages with their replacement.

* guix/packages.scm (package-superseded, deprecated-package): New
procedures.
* gnu/packages.scm (%find-package): Check for 'package-superseded'.
* guix/scripts/package.scm (transaction-upgrade-entry)[supersede]: New
procedure.  Call it when 'package-superseded' is true.
* tests/guix-build.sh: Add test for a superseded package.
* tests/packages.scm ("package-superseded")
("transaction-upgrade-entry, superseded package"): New tests.

guix package: Build up the transaction incrementally.

* guix/scripts/package.scm (upgraded-manifest-entry): Rename to...
(transaction-upgrade-entry): ... this.  Add 'transaction' parameter and
return a transaction.
(options->installable): Likewise.
[to-upgrade]: Rename to...
[upgraded]: ... this, and change to be a transaction.  Return a
transaction.
(options->removable): Likewise.
(process-actions): Adjust accordingly.
* tests/packages.scm ("transaction-upgrade-entry, zero upgrades")
("transaction-upgrade-entry, one upgrade"): New tests.

guix package: Clarify upgrade code.

* guix/scripts/package.scm (upgradeable?): Rename to...
(upgraded-manifest-entry): ... this.  Change to take a <manifest-entry>
and to return a <manifest-entry>.
(options->installable)[to-upgrade]: Adjust accordingly.

guix build: Rewrite '--with-input' in terms of 'package-input-rewriting'.

* guix/scripts/build.scm (transform-package-inputs): Rewrite in terms of
'package-input-rewriting'.

services: shepherd: Add 'shepherd-service-upgrade', from 'guix system'.

* guix/scripts/system.scm (service-upgrade): Move to...
* gnu/services/shepherd.scm (shepherd-service-upgrade): ... here.
* tests/system.scm ("service-upgrade: nothing to do", "service-upgrade:
one unchanged, one upgraded, one new", "service-upgrade: service
depended on is not unloaded", "service-upgrade: obsolete services that
depend on each other"): Move to...
* tests/services.scm: ... here.  Adjust to 'service-upgrade' rename.

guix system: Do not unload services depended on.

Reported by Mark H Weaver <mhw@netris.org>
at <https://lists.gnu.org/archive/html/guix-devel/2016-08/msg01470.html>.

* guix/scripts/system.scm (service-upgrade)[live-service-required?]: New
procedure.
[obsolete?]: Use it.
* tests/system.scm ("service-upgrade: service depended on is not
unloaded", "service-upgrade: obsolete services that depend on each
other"): New tests.

guix system: Use 'shepherd-service-lookup-procedure' in 'service-upgrade'.

* guix/scripts/system.scm (service-upgrade)[essential?]: SERVICE is now
a <live-service>.
[lookup-target, lookup-live, running?, stopped, obsolete?]: New
procedures.
[to-load, to-unload]: Use them.  TO-UNLOAD is now a list of
<live-service>.
(call-with-service-upgrade-info): Extract symbols from TO-UNLOAD.
* tests/system.scm ("service-upgrade: one unchanged, one upgraded, one
new"): Adjust accordingly.