* gnu/packages/java.scm (ant)[source]: Use Apache mirror instead of
  plain URL.

Fixes CVE-2015-{7575, 8126, 8472} and CVE-2016-{0402, 0448, 0466, 0483,
0494}.

* gnu/packages/java.scm (icedtea-7): Update to 2.6.4.

Fixes CVE-2015-{8126, 8472} and CVE-2016-{0402, 0448, 0466, 0483, 0494}.

* gnu/packages/java.scm (icedtea-6): Update to 1.13.10.

* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory
  prefix in the "unpack" phase to "icedtea6-".

* gnu/packages/java.scm (icedtea7): Rename variable to...
(icedtea-7): ...this.
(icedtea): Refer to "icedtea-7".

* gnu/packages/java.scm (icedtea6): Rename variable to...
(icedtea-6): ...this.

* gnu/packages/java.scm (icedtea6): Change package name to "icedtea".
(icedtea7): Inherit package name.

* gnu/packages/java.scm (icedtea): New variable.
(swt)[native-inputs]: Replace "icedtea6" with "icedtea".
* gnu/packages/bioinformatics.scm (htsjdk)[native-inputs]: Likewise.
(ngs-java)[inputs]: Likewise.
* gnu/packages/kodi.scm (kodi)[native-inputs]: Replace "icedtea7" with
"icedtea".
* gnu/packages/ruby.scm (ruby-rjb)[native-inputs]: Replace "icedtea7"
with "icedtea".

* gnu/packages/java.scm (icedtea6)[arguments]: Unpack OpenJDK sources to
"openjdk.src".
(icedtea7)[arguments]: Inherit "--with-openjdk-src-dir" flag; refer to
"openjdk.src" in build phases; simplify "unpack" phase.
[native-inputs]: Rename "openjdk-drop" to "openjdk-src".

* gnu/packages/java.scm (icedtea7): Update to 2.6.3.

* gnu/packages/java.scm (icedtea6): Update to 1.13.9.

* gnu/packages/java.scm (ant): Update to 1.9.6.

* gnu/packages/java.scm (icedtea7): Update to 2.6.2.

* gnu/packages/java.scm (icedtea6): Update to 1.13.8.

* gnu/packages/java.scm (icedtea6)[native-inputs]: Replace
  "ant-bootstrap" with "ant".
  [arguments]: Remove steps to unpack and use "ant-bootstrap".
  (icedtea7)[native-inputs]: Remove explicit references to
  "ant-bootstrap" and "ant".

* gnu/packages/java.scm (ant)[native-inputs]: Replace "icedtea6" with
  "gcj".

* gnu/packages/gcc.scm (gcj-4.8): Inherit from "gcc" package and rename
  variable to...
  (gcj): ...this new variable.
  (ecj-bootstrap-4.8): Rename variable to...
  (ecj-bootstrap): ...this, updating to version 4.9.
* gnu/packages/java.scm (icedtea6)[native-inputs]: Replace "gcj-4.8"
  with "gcj".
* gnu/packages/music.scm (tuxguitar)[native-inputs]: Likewise.

* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
  plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
  Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.

* gnu/packages/java.scm (icedtea7): Update to 2.6.1.

* gnu/packages/java.scm (icedtea7): Bootstrap with GCJ rather than compile
  with IcedTea6.

* gnu/packages/java.scm (gcj-4.8)[arguments]: Add target-dependent GCJ include
  directory to CPATH environment variable.

* gnu/packages/java.scm (icedtea7): New variable.

* gnu/packages/java.scm (icedtea6)[arguments]: Split phase 'fix-tests into
  three phases 'fix-test-framework, 'fix-hotspot-tests, and 'fix-jdk-tests.

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

* gnu/packages/java.scm (icedtea6): Update to version 1.13.7.

* gnu/packages/haskell.scm (ghc)[arguments]: Add #:validate-runpath?.
* gnu/packages/julia.scm (julia)[arguments]: Likewise.
* gnu/packages/java.scm (icedtea6)[arguments]: Likewise.

* gnu/packages/java.scm (icedtea6): Remove commented substitution.

* gnu/packages/java.scm (icedtea6)[arguments]: Do not set CC and
  LD_LIBRARY_PATH variables.

* gnu/packages/java.scm (icedtea6)[arguments]: Rename ‘set-paths’ phase to
  ‘set-additional-paths’.

* gnu/packages/java.scm (icedtea6)[arguments]: Move patching of patches from
  ‘patch-paths’ to new ‘patch-patches’ phase.

* gnu/packages/java.scm (icedtea6)[arguments]: patch Makefile to override
  DEF_OBJCOPY variable definition.

* gnu/packages/java.scm (icedtea6)[arguments]: patch bootstrap ant in the
  `unpack' phase instead of `patch-paths'.

* gnu/packages/which.scm: Remove.
* gnu-system.am (GNU_SYSTEM_MODULES): Remove it.
* gnu/packages/base.scm (which): New variable.
* gnu/packages/aspell.scm, gnu/packages/audio.scm,
  gnu/packages/autogen.scm, gnu/packages/cdrom.scm,
  gnu/packages/compression.scm, gnu/packages/datamash.scm,
  gnu/packages/games.scm, gnu/packages/glib.scm,
  gnu/packages/gnu-pw-mgr.scm, gnu/packages/gnutls.scm,
  gnu/packages/gps.scm, gnu/packages/guile.scm,
  gnu/packages/java.scm, gnu/packages/libevent.scm,
  gnu/packages/linux.scm, gnu/packages/lisp.scm,
  gnu/packages/node.scm, gnu/packages/ntp.scm,
  gnu/packages/orpheus.scm, gnu/packages/pciutils.scm,
  gnu/packages/python.scm, gnu/packages/qt.scm,
  gnu/packages/rsync.scm, gnu/packages/sawfish.scm,
  gnu/packages/scheme.scm, gnu/packages/ssh.scm,
  gnu/packages/statistics.scm, gnu/packages/texlive.scm,
  gnu/packages/wdiff.scm: Adjust accordingly.

* gnu/packages/java.scm (icedtea6)[outputs]: Use separate outputs for
  documentation ("doc"), JDK ("jdk"), and JRE ("out").
* gnu/packages/java.scm (ant)[native-inputs]: Reference "jdk" output of
  icedtea6 package.
* gnu/packages/statistics.scm (r)[inputs]: Reference "jdk" output of icedtea6
  package.

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

* gnu/packages/java.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.