* gnu/packages/linux.scm (module-init-tools)[source](patches): New
field.
* gnu/packages/patches/module-init-tools-moduledir.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/system.scm (etc-directory): Add #:kernel parameter. Set
'LINUX_MODULE_DIRECTORY' in bashrc.
(operating-system-etc-directory): Pass #:kernel to 'etc-directory'.
* gnu/packages/linux.scm (util-linux)[source](patches): New field.
* gnu/packages/patches/util-linux-perl.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/version-control.scm (cssc): New variable.
* gnu/packages/patches/cssc-gets-undeclared.patch: New file
* gnu/packages/patches/cssc-missing-include.patch: New file
* gnu-system.am: Add gnu/packages/patches/cssc-gets-undeclared.patch
and gnu/packages/patches/cssc-missing-include.patch
* gnu.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
* build-aux/hydra/demo-os.scm: Use (gnu) and strip import list
accordingly.
* doc/guix.texi (Using the Configuration System): Adjust example
accordingly.
This fixes a circular dependency between (gnu system) and (gnu system
linux-initrd), where the latter could end up being compiled before
'file-system-type' was defined as a macro.
* gnu/system.scm (<file-system>, %fuse-control-file-system,
%binary-format-file-system): Move to...
* gnu/system/file-systems.scm: ... here. New file.
* build-aux/hydra/demo-os.scm, gnu/system/linux-initrd.scm,
gnu/system/vm.scm: Use it.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/maths.scm (superlu-dist): New variable.
* gnu/packages/patches/superlu-dist-scotchmetis.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/maths.scm (scotch): New variable.
* gnu/packages/patches/scotch-test-threading.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/patches/perl-tk-x11-discover.patch: New patch.
* gnu-system.am [dist_patch_DATA]: Add it.
* gnu/packages/tcl.scm (perl-tk)[origin]: Use it.
* gnu/packages/maths.scm (petsc): New variable.
(petsc-complex): New variable.
* gnu/packages/patches/petsc-fix-threadcomm.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/rdf.scm (soprano): Add input clucene and patch the cmake
file looking for it.
* gnu/packages/patches/soprano-find-clucene.patch: New file.
* gnu-system.am (dist_patch_DATA): Register the patch.
* gnu/packages/doxygen.scm: New file.
* gnu/packages/patches/doxygen-test.patch,
gnu/packages/patches/doxygen-tmake.patch: New files.
* gnu-system.am (GNU_SYSTEM_MODULES, dist_patch_DATA): Register the new files.
* gnu/packages/patches/python-libffi-mips-n32-fix.patch: New file.
* gnu/packages/python.scm (python-2, python): Add it.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/patches/libssh-CVE-2014-0017.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/ssh.scm (libssh-0.5): New variable.
(guile-ssh): Use it.
Based on a patch by Dan Kennedy <danielk1977@gmail.com>.
* gnu/packages/patches/sqlite-large-page-size-fix.patch: New file.
* gnu/packages/sqlite.scm (sqlite): Add it.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/patches/python-fix-dbm.patch: remove file. It is not needed
anymore, and is probably a left-over of a failed merge.
* gnu-system.am: remove gnu/packages/patches/python-fix-dbm.patch
* gnu/packages/patches/coreutils-skip-nohup.patch: patch taken from the git
repository of coreutils, that makes sure tests/misc/nohup.sh does not fail
when /dev/tty does not exist.
* gnu/packages/base.scm (coreutils): use it.
* gnu-system.am (dist_patch_DATA): add it.
Mark H Weaver