gnu: Add freefall.

* gnu/packages/linux.scm (freefall): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: mariadb: Update to 10.1.12.

* gnu/packages/databases.scm (mariadb): Update to 10.1.12.

build: Do not remake doc/guix.1.

* doc.am (doc/guix.1): Do not depend on $(sub_commands_mans) which will
  always appear out-of-date.

gnu: petsc: Fix compiler configuration references.

* gnu/packages/maths.scm (petsc)[arguments]: When patching compiler
  driver paths, do not assume they come from fortran input.

gnu: slepc: Set origin file-name.

* gnu/packages/maths.scm (slepc)[source]: Add file-name.

gnu: Fix definitions of gcc-toolchain-4.8 and gcc-toolchain-4.9.

* gnu/packages/commencement.scm (gcc-toolchain-4.8): Use gcc-4.8,
not gcc-final.
(gcc-toolchain-4.9): Use gcc-final, not gcc-4.9.
* gnu/packages/gcc.scm (gcc): Add reminder comment for the future.

gnu: guix: Update development snapshot to 71e2065.

* gnu/packages/package-management.scm (guix-devel): Update to 71e2065.

gnu: offlineimap: Update to 6.7.0.

* gnu/packages/mail.scm (offlineimap): Update to 6.7.0.

substitute: Honor client-provided empty URL list.

Before that, 'guix build --substitute-urls=""' would lead to using the
daemon's own URL list instead of the empty list.  The 'or*' hack, which
is to blame, had become unnecessary since commit
fb4bf72be3fbc23bca35ba4b842b7e1517ef0e3a.

Reported by Mark H Weaver <mhw@netris.org>.

* guix/scripts/substitute.scm (or*): Remove.
(%cache-urls): Use 'or' instead of 'or*'.
* tests/store.scm ("substitute query, alternating URLs"): Add test with
empty URL list.
* doc/guix.texi (Common Build Options): Mention the empty string.

build: Write emacs-autoloads.el to $(builddir).

* emacs.am ($(AUTOLOADS)): Write to $(builddir), not $(srcdir).

substitute: Honor the 'max-age' of 'Cache-Control' headers.

This allows substitute servers to tell 'guix substitute' how long they
can cache narinfo lookups.

* guix/scripts/substitute.scm (cache-narinfo!): Add 'ttl' parameter.
[cache-entry]: Honor it.
(fetch-narinfos)[handle-narinfo-response]: Check the 'Cache-Control'
header of RESPONSE and pass its 'max-age' value to 'cache-narinfo!'.

substitute: Make room for a 'ttl' field in cached entries.

* guix/scripts/substitute.scm (cached-narinfo): Expect 'narinfo' sexp
version 2 with a 'ttl' field.
(cache-narinfo!)[cache-entry]: Produce 'narinfo' sexp version 2 with a
'ttl' field.
(remove-expired-cached-narinfos)[expired?]: Read 'narinfo' sexp version 2.

gnu: cm: Update to 0.3.

* gnu/packages/algebra.scm (cm): Update to 0.3.
  [license]: Change to gpl3+.

build: Default to "https://mirror.hydra.gnu.org/" for substitutes.

* config-daemon.ac: Check for (gnutls) and define 'GUIX_SUBSTITUTE_URLS'.
* nix/nix-daemon/guix-daemon.cc (main): Use GUIX_SUBSTITUTE_URLS.
* guix/store.scm (%default-substitute-urls): Use 'https' when (gnutls)
is available.
* doc/guix.texi (Binary Installation): Mention mirrors
(Invoking guix-daemon): Mention mirror.hydra.gnu.org.
(Substitutes): Mention mirrors.
(Invoking guix archive): Show https URLs.

http-client: No 'setvbuf' for non-file ports.

* guix/http-client.scm (http-fetch): Do not call 'setvbuf' on non-file
ports.

gnu: Add r-dnacopy.

* gnu/packages/bioinformatics.scm (r-dnacopy): New variable.

gnu: Add codingquarry.

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

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add idle3-tools.

* gnu/packages/disk.scm (idle3-tools): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: neon: Update to 0.30.1.

* gnu/packages/version-control.scm (neon): Update to 0.30.1.

gnu: mercurial: Update to 3.7.2.

* gnu/packages/version-control.scm (mercurial): Update to 3.7.2.
[source]: Update to mercurial-scm.org.
[home-page]: Same.