gnu: icedtea-8: Install the nss.cfg file to JRE.

Before this, accessing HTTPS will throw an exception about 'nss.cfg' could not
be found.

* gnu/packages/java.scm (icedtea-8)[arguments]: Copy 'nss.cfg' from JDK into
JRE in the install phase.

gnu: classpath-devel: Fix build after d10092b8491.

* gnu/packages/java.scm (classpath-devel)[arguments]: Actually run 'bootstrap'
phase.

gnu: Put autoconf-related phases immediately after the 'unpack phase.

* gnu/packages/audio.scm (audacity, rtmidi)[arguments]: Correct phases
accordingly.
* gnu/packages/bioinformatics.scm (mash, seek, vsearch, emboss,
htslib-for-sambamba)[arguments]: Likewise.
* gnu/packages/ci.scm (cuirass)[arguments]: Likewise.
* gnu/packages/compression.scm (minizip, xdelta)[arguments]: Likewise.
* gnu/packages/cpp.scm (libzen)[arguments]: Likewise.
* gnu/packages/crypto.scm (opendht)[arguments]: Likewise.
* gnu/packages/databases.scm (4store, mdbtools)[arguments]: Likewise.
* gnu/packages/debug.scm (stress-make)[arguments]: Likewise.
* gnu/packages/dns.scm (dnscrypt-proxy, dnscrypt-wrapper)[arguments]:
Likewise.
* gnu/packages/emacs.scm (emacs-pdf-tools)[arguments]: Likewise.
* gnu/packages/embedded.scm (libjaylink, openocd)[arguments]: Likewise.
* gnu/packages/engineering.scm (gerbv)[arguments]: Likewise.
* gnu/packages/erlang.scm (erlang)[arguments]: Likewise.
* gnu/packages/ftp.scm (weex)[arguments]: Likewise.
* gnu/packages/gnome.scm (dia)[arguments]: Likewise.
* gnu/packages/gnunet.scm (gnurl, guile-gnunet)[arguments]: Likewise.
* gnu/packages/gtk.scm (guile-rsvg, graphene)[arguments]: Likewise.
* gnu/packages/guile.scm (guildhall, guile-ics, guile-sqlite3)[arguments]:
Likewise.
* gnu/packages/ibus.scm (ibus-libpinyin)[arguments]: Likewise.
* gnu/packages/irc.scm (weechat)[arguments]: Likewise.
* gnu/packages/java.scm (classpath-devel)[arguments]: Likewise.
* gnu/packages/libreoffice.scm (libetonyek)[arguments]: Likewise.
* gnu/packages/libusb.scm (hidapi)[arguments]: Likewise.
* gnu/packages/linux.scm (gpm)[arguments]: Likewise.
* gnu/packages/logging.scm (glog)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Likewise.
* gnu/packages/mail.scm (dovecot-trees, dovecot-libsodium-plugin, esmtp)
[arguments]: Likewise.
* gnu/packages/messaging.scm (freetalk, libmesode, libstrophe)[arguments]:
Likewise.
* gnu/packages/microcom.scm (microcom)[arguments]: Likewise.
* gnu/packages/ocaml.scm (ocaml-ssl)[arguments]: Likewise.
* gnu/packages/parallel.scm (slurm)[arguments]: Likewise.
* gnu/packages/pdf.scm (libharu)[arguments]: Likewise.
* gnu/packages/samba.scm (cifs-utils)[arguments]: Likewise.
* gnu/packages/serialization.scm (msgpack)[arguments]: Likewise.
* gnu/packages/shells.scm (scsh)[arguments]: Likewise.
* gnu/packages/telephony.scm (libiax2)[arguments]: Likewise.
* gnu/packages/textutils.scm (dotconf)[arguments]: Likewise.
* gnu/packages/version-control.scm (findnewest)[arguments]: Likewise.
* gnu/packages/video.scm (libmediainfo, mediainfo)[arguments]: Likewise.

gnu: java-slf4j-api: Fix tests.

* gnu/packages/java.scm (java-slf4j-api)[arguments]: Enable tests
Adjust the jar content to prevent a test failure.

gnu: Give descriptive file-names for some Git sources.

* gnu/packages/java.scm (classpath-devel)[source]: Set the file-name.
* gnu/packages/guile.scm (guile-for-guile-emacs,
guile-syntax-highlight)[source]: Likewise.

gnu: Fetch several Git sources over HTTPS.

* gnu/packages/admin.scm (interrobang)[source]: Use HTTPS URL.
* gnu/packages/audio.scm (ardour)[source]: Likewise.
* gnu/packages/embedded.scm (libjaylink, openocd)[source]: Likewise.
* gnu/packages/gnome.scm (byzanz)[source]: Likewise.
* gnu/packages/gnunet.scm (guile-gnunet)[source]Likewise.
* gnu/packages/java.scm (classpath)[source]: Likewise.
* gnu/packages/microcom.scm (microcom)[source]: Likewise.
* gnu/packages/python.scm (python-axolotl-curve25519)[source]: Likewise.
* gnu/packages/rdesktop.scm (freerdp)[source]: Likewise.
* gnu/packages/shells.scm (rc)[source]: Likewise.
* gnu/packages/web.scm (libwebsockets)[source]: Use new source URL.

Merge branch 'core-updates'

Merge branch 'master' into core-updates

gnu: icedtea@3: Update to 3.5.1.

* gnu/packages/java.scm (icedtea-8): Update to 3.5.1.

gnu: icedtea@2: Update to 2.6.11 [security fixes].

Fixes CVE-2017-{10053,10067,10074,10081,10087,10089,10090,10096,10101,10102,
10107,10108,10109,10110,10111,10115,10116,10118,10135,10074,10176}.

* gnu/packages/java.scm (icedtea-7): Update to 2.6.11.

gnu: icedtea@3.5.0: Properly handle decoding error while substituting.

* gnu/packages/java.scm (icedtea-8)[arguments] <patch-jni-libs>: Change
'encoding-error to 'decoding-error, which is what Guile 2.2 raises when
failing to decode an input file.

Merge branch 'master' into core-updates

gnu: icedtea@3: Update to 3.5.0 [security fixes].

Fixes CVE-2017-{10053,10067,10074,10074,10078,10081,10087,10089,10090,10096,
10101,10102,10107,10108,10109,10110,10111,10115,10116,10118,10135,10176,10193,
10198}.

* gnu/packages/java.scm (icedtea-8): Update to 3.5.0.

gnu: Add java-commons-cli@1.2.

* gnu/packages/java.scm(java-commons-cli-1.2): New variable.

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

Merge branch 'master' into core-updates

gnu: Add java-slf4j-api.

* gnu/packages/java.scm (java-slf4j-api): New variable.

gnu: Add java-javaewah.

* gnu/packages/java.scm (java-javaewah): New variable.

gnu: Add java-classpathx-servletapi

* gnu/packages/java.scm (java-classpathx-servletapi): New variable.

Merge branch 'master' into core-updates

gnu: clojure: Update "tools-reader-src" to 1.0.0.

* gnu/packages/java.scm (clojure)[inputs]: Update "tools-reader-src" to
1.0.0.

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