* guix/scripts/environment.scm (create-environment): Define 'GUIX_ENVIRONMENT'.
* doc/guix.texi (Invoking guix environment): Document it.
* gnu/system/shadow.scm (default-skeletons): Adjust 'PS1' depending on whether
  'GUIX_ENVIRONMENT' is defined.

* doc/guix.texi (Invoking guix environment): Add footnote about .bashrc
  vs. .bash_profile.

This fixes two problems:

  1. Load errors would print an ugly backtrace.
  2. When FILE was an absolute name, 'load' was passed an incorrect file
     name.

* guix/scripts/environment.scm (options/resolve-packages): Use 'load*' instead
  of 'load'.

* guix/scripts/environment.scm (package+propagated-inputs): Add 'output'
  parameter.  Use it in return value.
  (options/resolve-packages): Use 'append-map' instead of 'map'.  For 'load'
  and 'expression', return all the outputs of the resulting package.  For
  'package', use 'specification->package+output' instead of
  'specification->package'.
  (guix-environment): Adjust uses of PACKAGES accordingly.
* doc/guix.texi (Invoking guix environment): Document it.
* tests/guix-environment.sh: Add test for --ad-hoc guile-bootstrap:out.

* guix/scripts/environment.scm (show-help, %options): Add -s/--system.
  (%default-options): Add 'system' pair.
  (guix-environment): Pass 'system' value from OPTS to 'lower-inputs'.
* doc/guix.texi (Invoking guix environment): Document it.

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.