Before that, 'guix environment guile' (for instance) would define environment
variables that would refer to the "include" output of Bash, the "debug" output
of libgc, etc., even though these are not listed as inputs in the recipe of
'guile'.

* guix/gexp.scm (lower-inputs): Export.
* guix/scripts/environment.scm (evaluate-input-search-paths): Remove
  'derivations' parameter; add 'search-paths'.  Expect 'inputs' to be
  a list of tuples.  Adjust callers.
  (create-environment): Remove 'derivations' parameter; add 'search-paths'.
  (show-search-paths): Likewise.
  (package+propagated-inputs): New procedure.
  (packages->transitive-inputs, packages+propagated-inputs): Remove.
  (build-inputs): Expect INPUTS to be a list of derivation tuples.
  (guix-environment): Compute INPUTS using 'package+propagated-inputs',
  'package->bag', and 'bag-transitive-inputs'.  Move 'run-with-store' higher.
* tests/guix-environment.sh: Add test with FINDUTILS-BOOT0.

* tests/guix-environment.sh: New file.
* Makefile.am (SH_TESTS): Add it.

* gnu/packages/music.scm (powertabeditor)[inputs]: Replace "gcc" with
  "libiberty".

* gnu/packages/music.scm (hydrogen): New variable.

* gnu/packages/linux.scm (linux-libre): Update to 4.1.1.

* gnu/packages/version-control.scm (package-transitive-propagated-labels*)
  (package-propagated-input-refs): New procedures.
  (git)[inputs]: Add perl-authen-sasl, perl-net-smtp-ssl, and perl-io-socket-ssl.
  [outputs]: Add send-email output.
  [arguments]: Add #:modules argument with srfi-1.  In 'split phase, wrap
  git-send-email.

* gnu/packages/web.scm (perl-authen-sasl): New variable.

* gnu/packages/web.scm (perl-gssapi): New variable.

* gnu/packages/web.scm (perl-net-smtp-ssl): New variable.

* gnu/packages/curl.scm (arguments): Disable test 1510.

* gnu/packages/curl.scm (curl): Update to 7.43.0.

* gnu/packages/maths.scm (dealii, dealii-openmpi): New variables.
* gnu/packages/patches/dealii-p4est-interface.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.

* gnu/packages/maths.scm (slepc, slepc-complex, slepc-openmpi)
  (slepc-complex-openmpi): New variables.

* gnu/packages/maths.scm (arpack-ng-openmpi): New variable.

* gnu/packages/maths.scm (petsc): Upgrade to 3.6.0.
* gnu/packages/patches/petsc-fix-threadcomm.patch: Delete patch.
* gnu-system.am (dist_patch_DATA): Remove it.

* gnu/packages/maths.scm (mumps, mumps-metis, mumps-openmpi)
  (mumps-metis-openmpi): New variables.
* gnu/packages/patches/mumps-build-parallelism.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.

* gnu/packages/maths.scm (metis): New variable.

* gnu/packages/maths.scm (p4est, p4est-openmpi): New variables.

* gnu/packages/maths.scm (scalapack): New variable.

* gnu/packages/maths.scm (scotch)[arguments]: Add 'build-esmumps
  phase.  Install esmumps libraries and headers in 'install phase.
  (pt-scotch)[arguments]: Build ptesmumps in 'build phase.  Add
  make parallelism.

* gnu/packages/maths.scm (scotch, pt-scotch)[arguments]: Use modify-phases.

* gnu/packages/maths.scm (scotch): Update to 6.0.4.
  [arguments]: Add -fPIC to CFLAGS.
* gnu/packages/patches/scotch-test-threading.patch: Adjust patch for a
  new set of test fixes.
* gnu/packages/patches/pt-scotch-build-parallelism.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.

* gnu/packages/mpi.scm (openmpi): Upgrade to 1.8.5.
  [native-inputs]: Add perl.
  [arguments]: Add configure flags for thread support.

* gnu/packages/mpi.scm (hwloc)[propagated-inputs]: Move numactl from here...
  [inputs]: ...to here.
  [arguments]: New 'refine-libnuma' phase.

* gnu/packages/patches/hwloc-gather-topology-lstopo.patch: New patch.
* gnu/packages/mpi.scm (hwloc): Upgrade to 1.10.1.
  [source]: Use patch.
  [propagated-inputs]: Remove libpci.
  [inputs]: Add libpciaccess.
* gnu-system.am (dist_patch_DATA): Add patch.

* gnu/packages/python.scm (python-mccabe)[license]: 'expat' ->
  'license:expat'.

* gnu/packages/python.scm (python-flake8, python2-flake8): New variables.

* gnu/packages/python.scm (python-mccabe, python2-mccabe): New variables.

* gnu/packages/python.scm (python-pyflakes, python2-pyflakes): New variables.

* gnu/packages/python.scm (python-pep8, python2-pep8): New variables.

* doc/environment-gdb.scm: New file.
* doc.am (EXTRA_DIST): Add it.
* doc/guix.texi (Invoking guix environment): Clarify wording of the first
  example.  Add a --ad-hoc example upfront.  Add an example for '-e', and one
  for '-l'.

* gnu/packages/code.scm (withershins)[inputs]: Replace "gcc" with "libiberty".
   [arguments]: Simplify "find-libiberty" phase.

* gnu/packages/gcc.scm (make-libiberty, libiberty): New variables.

* gnu/packages/statistics.scm (r): Update to 3.2.1.
* gnu/packages/patches/r-fix-15899.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.

* gnu/packages/bioinformatics.scm (blast+): New variable.

* gnu/packages/code.scm (global): Update to 6.5.

* gnu/packages/man.scm (help2man): Update to 1.47.1.

* gnu/packages/parallel.scm (parallel): Update to 20150622.

* gnu/packages/screen.scm (screen): Update to 4.3.1.

* gnu/packages/texinfo.scm (texinfo-6): New variable.