* gnu/packages/apl.scm (apl): Upgrade to 1.3.

* gnu/packages/cdrom.scm (xorriso): Upgrade to 1.3.6.pl01.

* gnu/packages/gxmessage.scm (gxmessage): Upgrade to 2.20.1.

* gnu/packages/help2man.scm (help2man): Upgrade to 1.45.1.

* gnu/packages/zile.scm (zile): Upgrade to 2.4.11.

* gnu/packages/maths.scm (units): Upgrade to 2.11.

* gnu/packages/freeipmi.scm (freeipmi): Upgrade to 1.4.1.

* gnu/packages/parallel.scm (parallel): Upgrade to 20140322.

* gnu/packages/xnee.scm (xnee): Upgrade to 3.18.

* gnu/packages/maths.scm (glpk): Upgrade to 4.54.

Fixes bug introduced in d4bf49b1.

* gnu/packages/texlive.scm (texlive): Change 'alist-replace' to
  'alist-cons-before'.

* tests/union.scm ("union-build with symlink to directory"): New test.

* guix/build/union.scm: Rewrite; only 'file=?' remains unchanged.  Remove
  'tree-union' and 'delete-duplicate-leaves' exports.  Merge inputs in a
  breadth-first fashion.  Follow symlinks for purposes of making decisions
  about the merge.

* tests/union.scm: Remove tests of 'tree-union' and 'delete-duplicate-leaves'.

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/sqlite.scm (sqlite): Upgrade to 3.8.4.2.

* gnu/packages/sqlite.scm (sqlite): Compute the numeric-version from the
  traditional version string, and use it to compute the source URL.

* gnu/packages/mail.scm (mutt): Upgrade to 1.5.23.  Add bitbucket
  source URL and try it first.

* gnu/packages/version-control.scm (bazaar): Add a phase that
  fixes setup.py to install man pages in share/man.

* gnu/packages/ocaml.scm (ocaml): Pass -mandir to configure.

* gnu/packages/pth.scm (pth): Add --mandir to configure flags.

* gnu/packages/tcl.scm (expect): Add --mandir configure flag.
  Use 'let' to simplify configure flags generation.

* gnu/packages/zip.scm (zip): Eliminate custom configure phase which copied
  and patched the Makefile.  Instead add "-f" and "prefix" to make-flags, as
  well as "MANDIR".  Remove "generic_gcc" from the make-flags, so that it will
  not be passed during other phases involving 'make'.  Instead replace the
  'build' phase with one that specifies the "generic_gcc" target.

* gnu/packages/lua.scm (lua): Use 'system*' instead of 'system'.
  Add INSTALL_MAN argument to 'make'.

* gnu/packages/indent.scm (indent): Add a phase to fix the docdir
  setting in doc/Makefile.in.

* guix/scripts/package.scm (search-path-environment-variables)[manifest-entry->package]:
  Use 'find-best-packages-by-name' instead of 'find-packages-by-name'.
  On a profile with 140 packages, this reduces execution time of this
  procedure from 5.8 seconds to 2.9 seconds (50% improvement.)

* guix/scripts/package.scm (maybe-register-gc-root): New procedure.
* tests/guix-package.sh (profile): Grep the output of "guix gc
  --list-live" in a couple of places.

* gnu/packages/linux.scm (net-tools): Add 'INSTALLNLSDIR' and 'mandir'
  variables to make flags.

* gnu/packages/ssh.scm (libssh): Upgrade to 0.6.3.

* gnu/packages/pulseaudio.scm: Set the 'CK_DEFAULT_TIMEOUT' environment
  variable to 120 in the 'pre-check' phase.  Suggested by Ludovic Courtès.

* gnu/packages/file.scm (file): Upgrade to 5.18.

* gnu/packages/guile.scm (guile-json)[source]: Add 'snippet'.

* guix/pki.scm (acl-entry-sexp, acl-sexp): Remove.
  (public-keys->acl, current-acl): Return a native sexp.
  (acl->public-keys, authorized-key?): Expect ACL to be a native sexp.
* guix/scripts/archive.scm (authorize-key): Convert ACL to
  canonical-sexp when writing it.

* guix/scripts/substitute-binary.scm (regexp-exec): Change formals
  to (rx str . rest).

* guix/scripts/substitute-binary.scm (guix-substitute-binary) <--query>:
  Cache the result of (current-acl); pass it to 'valid-narinfo?' calls.
  This saves 12% wall-clock time for "guix build emacs -n".

* gnu/packages/mail.scm (bogofilter): New variable.

* gnu/packages/guile.scm (guile-json): New variable.

* guix/nar.scm (restore-file-set)[assert-valid-signature]: Rewrite in
  terms of 'signature-case'.
* guix/scripts/substitute-binary.scm (narinfo-signature->canonical-sexp):
  Call 'leave' instead of 'raise' when SIGNATURE is invalid.
  (&nar-signature-error, &nar-invalid-hash-error): Remove.
  (assert-valid-signature): Add 'narinfo' parameter; remove 'port'.
  Rewrite in terms of 'signature-case' and 'leave'.  Mention NARINFO's
  URI in error messages.  Adjust caller.
  (narinfo-sha256): New procedure.
  (assert-valid-narinfo): Use it.
  (valid-narinfo?): Rewrite using 'narinfo-sha256' and
  'signature-case'.
* tests/substitute-binary.scm (assert-valid-signature,
  test-error-condition): Remove.
  ("corrupt signature data", "unauthorized public key", "invalid
  signature"): Remove.

* guix/pki.scm (%signature-status): New procedure.
  (signature-case): New macro.
* tests/pki.scm (%secret-key, %alternate-secret-key): New variables.
  ("signature-case valid-signature", "signature-case invalid-signature",
  "signature-case hash-mismatch", "signature-case unauthorized-key",
  "signature-case corrupt-signature"): New tests.

* guix/scripts/substitute-binary.scm (assert-valid-narinfo): Add
  #:verbose? parameter; when true, write "found valid signature".
  (valid-narinfo?): Pass #:verbose? #f.

* guix/scripts/archive.scm (authorize-key): Add 'mkdir-p' call.
  Reported by Alex Sassmannshausen <alex.sassmannshausen@gmail.com>.