gnu: Use HTTPS URLs for GitHub home-pages.

* gnu/packages/bioinformatics.scm, gnu/packages/emacs.scm,
gnu/packages/haskell.scm, gnu/packages/libffi.scm, gnu/packages/lisp.scm,
gnu/packages/ocaml.scm, gnu/packages/openstack.scm, gnu/packages/python.scm,
gnu/packages/ruby.scm, gnu/packages/shells.scm, gnu/packages/statistics.scm,
gnu/packages/xdisorg.scm: Use HTTPS URLs for all packages with a home-page on
GitHub.

Merge branch 'core-updates'

gnu: xonsh: Update to 0.5.9.

* gnu/packages/shells.scm (xonsh): Update to 0.5.9.

gnu: dash: Update to 0.5.9.1.

* gnu/packages/shells.scm (dash): Update to 0.5.9.1.
[source]: Use git-fetch.
[native-inputs]: Add autoconf and automake.
[arguments]: Add 'bootstrap' phase.

Merge branch 'master' into core-updates

Merge branch 'master' into python-tests

gnu: tcsh: Use modify-phases.

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

gnu: tcsh: Update to 6.20.00.

* gnu/packages/shells.scm (tcsh): Update to 6.20.00.
[source]: Remove 'tcsh-do-not-define-BSDWAIT.patch'.
[inputs]: Remove coreutils. Move autoconf to ...
[native-inputs]: ... here. Add perl.
* gnu/packages/patches/tcsh-fix-autotest.patch: Adjust patch to upstream
changes.
* gnu/packages/patches/tcsh-do-not-define-BSDWAIT.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: xonsh: Update to 0.5.5.

* gnu/packages/shells.scm (xonsh): Update to 0.5.5.

Merge remote-tracking branch 'origin/master' into core-updates

gnu: fish: Fix build after upstream changes.

The 2.5.0 release was incorrectly packaged, then fixed in place. This is,
in a way, a follow-up to commit 89eb56f05fa1561b09d1050147d968b98a16b07a.
See <https://github.com/fish-shell/fish-shell/issues/3807>.

Reported by ng0 <contact.ng0@cryptolab.net>.

* gnu/packages/shells.scm (fish)[source]: Update hash.
[native-inputs]: Remove autoconf, automake, and libtool.
[arguments]: Remove ‘bootstrap’ phase.

gnu: Add scsh.

* gnu/packages/shells.scm (scsh): New variable.

Merge branch 'master' into python-tests

Merge branch 'master' into core-updates

gnu: xonsh: Update to 0.5.3.

* gnu/packages/shell.scm (xonsh): Update to 0.5.3.

gnu: fish: Update to 2.5.0.

* gnu/packages/shells.scm (fish): Update to 2.5.0.
[native-inputs]: Add autoconf, automake, and libtool.
[arguments]: Add ‘bootstrap’ phase.

gnu: tcsh: Incorporate grafted patch.

* gnu/packages/shells.scm (tcsh)[replacement]: Remove field.
[source]: Add patch 'tcsh-fix-out-of-bounds-read.patch'.
(tcsh/fixed): Remove variable.

Merge branch 'master' into core-updates

gnu: Add es.

* gnu/packages/shells.scm (es): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: fish: Embed full path to Python.

Fixes <https://bugs.gnu.org/25467>.

* gnu/packages/shells.scm (fish)[arguments]: Rename phase "patch-bc" to
"embed-store-paths"; embed full path to Python.