gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.

* 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: icedtea7: Update to 2.6.1.

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

Merge branch 'master' into core-updates

Conflicts:
	gnu/packages/commencement.scm
	gnu/packages/xml.scm

gnu: icedtea7: Bootstrap with GCJ.

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

Merge branch 'master' into core-updates

Merge branch 'master' into gtk-rebuild

Conflicts:
	gnu/packages/gtk.scm

gnu: icedtea6: Add target-dependent include directory to CPATH.

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

Merge branch 'master' into core-updates

gnu: Add icedtea7.

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

gnu: icedtea6: Split test fixing phases.

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

Merge branch 'master' into core-updates.

gnu: Add SWT.

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

Merge branch 'core-updates'

Merge branch 'master' into core-updates

Conflicts:
	gnu-system.am
	gnu/packages/gstreamer.scm

gnu: icedtea6: Update to 1.13.7.

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

gnu: Disable RUNPATH validation for packages that use $ORIGIN.

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

Merge branch 'master' into core-updates

gnu: icedtea6: remove commented substitution.

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

gnu: icedtea6: Do not set CC and LD_LIBRARY_PATH.

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

gnu: icedtea6: Rename ‘set-paths’ phase to ‘set-additional-paths’

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