monads: Hide 'derivation-expression' and 'lower-inputs'.

* guix/monads.scm: Unexport 'lower-inputs' and 'derivation-expression'.
  (text-file*): Add comment about the switch to 'gexp->derivation'.
  (lower-inputs): Add comment about its doom.
  (derivation-expression): Likewise.
* guix/gexp.scm (lower-inputs*): Rename to...
  (lower-inputs): ... this.  Update callers.
* tests/monads.scm (derivation-expression): New procedure.
* doc/guix.texi (The Store Monad): Use 'gexp->derivation' instead of
  'derivation-expression'.  Remove documentation of
  'derivation-expression'.
* guix/ui.scm (read/eval): Use THE-ROOT-MODULE so that macros are
  properly expanded.
* tests/guix-build.sh: Use 'gexp->derivation' instead of
  'derivation-expression'.monads: Hide 'derivation-expression' and 'lower-inputs'.

linux-initrd: Rewrite using gexps.

* gnu/system/linux-initrd.scm (expression->initrd): Rename 'inputs'
  parameter to 'to-copy'.  Remove 'files-to-copy'.  Rewrite 'builder' as
  a gexp, and use 'gexp->derivation'.
  (qemu-initrd): Adjust accordingly.

system: Rewrite 'union' using gexps.

* gnu/system.scm (union): Rewrite using 'gexp->derivation'.

services: xorg: Rewrite using gexps.

* gnu/services/xorg.scm (xorg-start-command): Rewrite in terms of
  'gexp->script'.
  (xinitrc): Likewise.

system: grub: Rewrite using gexps.

* gnu/system/grub.scm (grub-configuration-file): Rewrite using
  'gexp->derivation'.
* gnu/system.scm (operating-system-derivation): Adjust accordingly.

system: Change 'file-union' to use gexps.

* gnu/system.scm (file-union): Make 'name' the first parameter; remove
  'inputs' parameter.  Rewrite using 'gexp->derivation'.
  (etc-directory): Adjust accordingly.
  (operating-system-derivation): Ditto.

services: Rewrite using gexps.

* gnu/services.scm (<service>)[inputs]: Remove.
* gnu/system.scm (links): Remove.
  (etc-directory): Add PASSWD and SHADOW to #:inputs.
  (operating-system-boot-script): Pass ETC to 'dmd-configuration-file'.
  (operating-system-derivation): Remove EXTRAS from the union.
* gnu/system/linux.scm (pam-service->configuration): Rewrite in terms of
  'gexp->derivation'.  Compute the contents on the build side.  Expect
  'arguments' to contain a list of gexps.
  (pam-services->directory): Rewrite in terms of 'gexp->derivation'.
  (unix-pam-service): Change 'arguments' to a list of one gexp.
* gnu/system/shadow.scm (<user-account>)[inputs]: Remove.
  [shell]: Change default value to a gexp.
  (passwd-file): Rewrite in terms of 'gexp->derivation'.  Compute
  contents on the build side.
* gnu/services/base.scm (host-name-service, mingetty-service,
  nscd-service, syslog-service, guix-service): Change 'start' and 'stop'
  to gexps; remove 'inputs' field.
  (guix-build-accounts): Change 'shell' field to a gexp.
* gnu/services/networking.scm (static-networking-service): Change
  'start' and 'stop' to gexps; remove 'inputs' field.
* gnu/services/xorg.scm (slim-service): Likewise.
* gnu/services/dmd.scm (dmd-configuration-file): Expect ETC to be a
  derivation.  Change 'config' to a gexp.  Use 'gexp->file' instead of
  'text-file'.
* doc/guix.texi (Defining Services): Update nscd example with gexps, and
  without 'inputs'.  Add xref to "G-Expressions".

vm: Rewrite support procedures to use gexps.

* gnu/system/vm.scm (%imported-modules): Remove.
  (expression->derivation-in-linux-vm): Remove 'inputs' parameter.
  Rename 'imported-modules' to 'modules'.  Rewrite using gexps and
  'gexp->derivation'.
  (qemu-image): Add 'qemu' parameter.  Pass NAME to
  'expression->derivation-in-linux-vm'.  Rewrite using gexps.  Remove
  #:inputs argument to 'expression->derivation-in-linux-vm'.
  (operating-system-default-contents): Rewrite using gexps.
* gnu/system.scm (operating-system-profile-derivation): Rename to...
  (operating-system-profile): ... this.  Adjust callers.
  (operating-system-profile-directory): Remove.

store: (direct-store-path? (%store-prefix)) returns #f.

* guix/store.scm (direct-store-path?): Return #f if PATH
  is (%store-prefix).
* tests/store.scm ("direct-store-path?"): Add test.

gnu: Use gexps in obvious places in (gnu system ...).

* gnu/system.scm (operating-system-boot-script): Use 'gexp->file'
  instead of 'text-file*'.
* gnu/system/vm.scm (expression->derivation-in-linux-vm): Likewise.
  (system-qemu-image/shared-store-script)[builder]: Turn into a gexp.
  Use 'gexp->derivation' instead of 'derivation-expression'.

Add (guix gexp).

* guix/gexp.scm: New file.
* tests/gexp.scm: New file.
* Makefile.am (MODULES): Add guix/gexp.scm.
  (SCM_TESTS): Add tests/gexp.scm.
* doc/guix.texi (Derivations): Add #:inputs in 'derivation' example.
  Mark 'build-expression->derivation' as deprecated, refer to
  "G-Expressions".  Remove paragraph about code strata.
  (G-Expressions): New node.

gnu: soprano: Add input clucene.

* 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: soprano: Upgrade to 2.9.4.

* gnu/packages/rdf.scm (soprano): Upgrade to 2.9.4.

guix: cmake: Add input and package libraries to the rpath, and adapt package
  definitions accordingly.

* guix/build/cmake-build-system.scm (configure): Add flags.
* gnu/packages/maths.scm (lapack): Drop special code.
* gnu/packages/ssh.scm (libssh): Drop special code.
* gnu/packages/slim.scm (slim): Drop special code and enable shared library.

Co-authored-by: Eric Bavier <bavier@member.fsf.org>

gnu: soprano: Add native input doxygen.

* gnu/packages/rdf.scm (soprano): Add native input doxygen.

gnu: doxygen: Add propagated input graphviz.

* gnu/packages/doxygen.scm (doxygen): Add propagated input graphviz.

gnu: libkate: Add native input doxygen and make input pkg-config native.

* gnu/packages/xiph.scm (libkate): Add native input doxygen.
    Make input pkg-config native.

gnu: libmpdclient: Add native input doxygen.

* gnu/packages/mpd.scm (libmpdclient): Add native input doxygen.

gnu: libdbusmenu-qt: Add native input doxygen for building the documentation,
  and make input qjson native.

* gnu/packages/kde.scm (libdbusmenu-qt): Add native input doxygen for
    building the documentation.
    Make input qjson native, as it is needed only for the tests.

gnu: Add doxygen.

* 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.