emacs: Add missing shell completions.

* emacs/guix-pcomplete.el (guix-pcomplete-complete-option-arg): Complete
  file name for '--install-from-file' option of 'guix package' command,
  and for '--file' and '--with-source' options of 'guix build' command.

gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605].

* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1.

gnu: samtools: Update to 1.3.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.

build: Use 127 as the Linux hash-bang limit.

Reported by taylanbayirli@gmail.com (Taylan Ulrich Bayırlı/Kammer).

* m4/guix.m4 (LINUX_HASH_BANG_LIMIT): Set to 127.

gnu: skribilo: Update to 0.9.3.

* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3.
[native-inputs]: New field.

doc: Fix typo in "Build Systems".

* doc/guix.texi (Build Systems): Remove extra 's'.

gnu: boost: Update to 1.60.0.

* gnu/packages/boost.scm (boost): Update to 1.60.0.
  [source]: Remove patch.
* gnu/packages/patches/boost-mips-avoid-m32.patch: Delete patch
* gnu-system.am (dist_patch_DATA): Remove patch.

Also fix dependent packages:

* gnu/packages/patches/csound-header-ordering.patch: New patch.
* gnu/packages/audio.scm (csound)[source]: Use it.
  [arguments]: Add 'set-flags phase.
* gnu/packages/patches/libcmis-fix-test-onedrive.patch: New patch.
* gnu/packages/libreoffice.scm (libcmis)[source]: Use it.
  (libreoffice)[arguments]: Add LDFLAGS to #:configure-flags.
  (librevenge)[inputs]: Move boost from here...
  [propogated-inputs]: to here.
  [arguments]: Add LDFLAGS to #:configure-flags.
* gnu/packages/patches/openimageio-boost-1.60.patch: New patch.
* gnu/packages/graphics.scm (openimageio): Use it.
* gnu-system.am (dist_patch_DATA): Add patches.

gnu: boost: Use modify-phases.

* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.

build: 'make check' errors out if file name limits would be hit.

* Makefile.am (SCM_TESTS, SH_TESTS, TESTS, AM_TESTS_ENVIRONMENT)
(SCM_LOG_COMPILER, SH_LOG_COMPILER, AM_SCM_LOG_FLAGS)
(AM_SH_LOG_FLAGS): Move within 'if CAN_RUN_TESTS'.
(check-local) [!CAN_RUN_TESTS]: New target.
* daemon.am (AM_TESTS_ENVIRONMENT, TESTS): Ditto.
* m4/guix.m4 (GUIX_CHECK_FILE_NAME_LIMITS): Add parameter and set it.

build: Warn against long hash bang lines for tests.

* m4/guix.m4 (GUIX_TEST_HASH_BANG_LENGTH): New macro.
(GUIX_CHECK_FILE_NAME_LIMITS): Use it.  Warn against long hash bang
lines in tests.

doc: Show bootstrapping at the package level.

* doc/images/bootstrap-packages.dot: New file.
* doc.am (DOT_FILES): Add it.
* doc/guix.texi (Bootstrapping): Show 'guix graph' commands.  Includes
'images/bootstrap-packages' and comment it.

gnu: sudo: Add fix for CVE-2015-5602.

* gnu/packages/patches/sudo-CVE-2015-5602.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/admin.scm (sudo)[source]: Add patch.

gnu: global: Use modify-phases syntax.

* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.

gnu: global: Update to 6.5.2.

* gnu/packages/code.scm (global): Update to 6.5.2.

gnu: icedtea-6: Fix directory name in "unpack" phase.

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

gnu: linux-libre: Update to 4.4.

* gnu/packages/linux.scm (linux-libre): Update to 4.4.
* gnu/packages/linux-libre-i686.conf,
  gnu/packages/linux-libre-x86_64.conf: Update from
  <https://jxself.org/git/kernel-configs.git>.

gnu: Add fxtract.

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

gnu: youtube-dl: Update to 2016.01.09.

* gnu/packages/video.scm (youtube-dl): Update to 2016.01.09.

gnu: gp2c: Update to 0.0.9pl5.

* gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5.

gnu: texlive: Use modify-phases syntax.

* gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases
  syntax.