NixOS
diff --git a/nixos/doc/manual/configuration/declarative-packages.xml b/nixos/doc/manual/configuration/declarative-packages.xml
@@ -19,6 +19,12 @@
   <command>nixos-rebuild switch</command>.
  </para>
 
+ <note>
+  <para>
+   Some packages require additional global configuration such as D-Bus or systemd service registration so adding them to <xref linkend="opt-environment.systemPackages"/> might not be sufficient. You are advised to check the <link xlink:href="#ch-options">list of options</link> whether a NixOS module for the package does not exist.
+  </para>
+ </note>
+
  <para>
   You can get a list of the available packages as follows:
 <screen>

diff --git a/nixos/doc/manual/release-notes/rl-2003.xml b/nixos/doc/manual/release-notes/rl-2003.xml
@@ -168,6 +168,12 @@ services.xserver.displayManager.defaultSession = "xfce+icewm";
      SDDM, GDM, or using the startx module which uses Xinitrc.
     </para>
    </listitem>
+   <listitem>
+    <para>
+     The Way Cooler wayland compositor has been removed, as the project has been officially canceled.
+     There are no more <literal>way-cooler</literal> attribute and <literal>programs.way-cooler</literal> options.
+    </para>
+   </listitem>
    <listitem>
     <para>
       The BEAM package set has been deleted. You will only find there the different interpreters.

diff --git a/nixos/modules/hardware/opengl.nix b/nixos/modules/hardware/opengl.nix
@@ -43,11 +43,11 @@ in
         description = ''
           Whether to enable OpenGL drivers. This is needed to enable
           OpenGL support in X11 systems, as well as for Wayland compositors
-          like sway, way-cooler and Weston. It is enabled by default
+          like sway and Weston. It is enabled by default
           by the corresponding modules, so you do not usually have to
           set it yourself, only if there is no module for your wayland
-          compositor of choice. See services.xserver.enable,
-          programs.sway.enable, and programs.way-cooler.enable.
+          compositor of choice. See services.xserver.enable and
+          programs.sway.enable.
         '';
         type = types.bool;
         default = false;

diff --git a/nixos/modules/module-list.nix b/nixos/modules/module-list.nix
@@ -159,7 +159,6 @@
   ./programs/venus.nix
   ./programs/vim.nix
   ./programs/wavemon.nix
-  ./programs/way-cooler.nix
   ./programs/waybar.nix
   ./programs/wireshark.nix
   ./programs/x2goserver.nix

diff --git a/nixos/modules/programs/way-cooler.nix b/nixos/modules/programs/way-cooler.nix
diff --git a/nixos/modules/rename.nix b/nixos/modules/rename.nix
@@ -27,6 +27,8 @@ with lib;
     (mkRemovedOptionModule [ "services.osquery" ] "The osquery module has been removed")
     (mkRemovedOptionModule [ "services.fourStore" ] "The fourStore module has been removed")
     (mkRemovedOptionModule [ "services.fourStoreEndpoint" ] "The fourStoreEndpoint module has been removed")
+    (mkRemovedOptionModule [ "programs" "way-cooler" ] ("way-cooler is abandoned by its author: " +
+      "https://way-cooler.org/blog/2020/01/09/way-cooler-post-mortem.html"))
 
     # Do NOT add any option renames here, see top of the file
   ];

diff --git a/nixos/modules/services/cluster/kubernetes/pki.nix b/nixos/modules/services/cluster/kubernetes/pki.nix
@@ -20,6 +20,7 @@ let
         size = 2048;
     };
     CN = top.masterAddress;
+    hosts = cfg.cfsslAPIExtraSANs;
   });
 
   cfsslAPITokenBaseName = "apitoken.secret";
@@ -66,6 +67,15 @@ in
       type = bool;
     };
 
+    cfsslAPIExtraSANs = mkOption {
+      description = ''
+        Extra x509 Subject Alternative Names to be added to the cfssl API webserver TLS cert.
+      '';
+      default = [];
+      example = [ "subdomain.example.com" ];
+      type = listOf str;
+    };
+
     genCfsslAPIToken = mkOption {
       description = ''
         Whether to automatically generate cfssl API-token secret,

diff --git a/nixos/modules/services/x11/desktop-managers/gnome3.nix b/nixos/modules/services/x11/desktop-managers/gnome3.nix
@@ -144,7 +144,7 @@ in
       services.gnome3.core-shell.enable = true;
       services.gnome3.core-utilities.enable = mkDefault true;
 
-      services.xserver.displayManager.sessionPackages = [ pkgs.gnome3.gnome-session ];
+      services.xserver.displayManager.sessionPackages = [ pkgs.gnome3.gnome-session.sessions ];
 
       environment.extraInit = ''
         ${concatMapStrings (p: ''
@@ -249,11 +249,17 @@ in
       services.system-config-printer.enable = (mkIf config.services.printing.enable (mkDefault true));
       services.telepathy.enable = mkDefault true;
 
-      systemd.packages = with pkgs.gnome3; [ vino gnome-session ];
+      systemd.packages = with pkgs.gnome3; [
+        gnome-session
+        gnome-shell
+        vino
+      ];
 
       services.avahi.enable = mkDefault true;
 
-      xdg.portal.extraPortals = [ pkgs.gnome3.gnome-shell ];
+      xdg.portal.extraPortals = [
+        pkgs.gnome3.gnome-shell
+      ];
 
       services.geoclue2.enable = mkDefault true;
       services.geoclue2.enableDemoAgent = false; # GNOME has its own geoclue agent

diff --git a/nixos/modules/services/x11/display-managers/gdm.nix b/nixos/modules/services/x11/display-managers/gdm.nix
@@ -174,6 +174,10 @@ in
       "f /run/gdm/.config/gnome-initial-setup-done 0711 gdm gdm - yes"
     ];
 
+    # Otherwise GDM will not be able to start correctly and display Wayland sessions
+    systemd.packages = with pkgs.gnome3; [ gnome-session gnome-shell ];
+    environment.systemPackages = [ pkgs.gnome3.adwaita-icon-theme ];
+
     systemd.services.display-manager.wants = [
       # Because sd_login_monitor_new requires /run/systemd/machines
       "systemd-machined.service"

diff --git a/pkgs/applications/editors/uberwriter/default.nix b/pkgs/applications/editors/uberwriter/default.nix
@@ -0,0 +1,54 @@
+{ stdenv, fetchFromGitHub, meson, ninja, cmake
+, wrapGAppsHook, pkgconfig, desktop-file-utils
+, appstream-glib, pythonPackages, glib, gobject-introspection
+, gtk3, webkitgtk, glib-networking, gnome3, gspell, texlive
+, haskellPackages}:
+
+let
+  pythonEnv = pythonPackages.python.withPackages(p: with p;
+    [ regex setuptools python-Levenshtein pyenchant pygobject3 pycairo pypandoc ]);
+  texliveDist = texlive.combined.scheme-medium;
+
+in stdenv.mkDerivation rec {
+  pname = "uberwriter";
+  version = "unstable-2019-11-29";
+
+  src = fetchFromGitHub {
+    owner  = pname;
+    repo   = pname;
+    rev    = "7606a55389f8516d9fed7927fa50ff8822ee9e38";
+    sha256 = "0ky001vs9nfvqf05h4q7fl0n8vsgim59z22i66a8sw6bqipv62sg";
+  };
+
+  nativeBuildInputs = [ meson ninja cmake pkgconfig desktop-file-utils
+    appstream-glib wrapGAppsHook ];
+
+  buildInputs = [ glib pythonEnv gobject-introspection gtk3
+    gnome3.adwaita-icon-theme webkitgtk gspell texliveDist
+    glib-networking ];
+
+  postPatch = ''
+    patchShebangs --build build-aux/meson_post_install.py
+
+    substituteInPlace uberwriter/config.py --replace "/usr/share/uberwriter" "$out/share/uberwriter"
+
+    # get rid of unused distributed dependencies
+    rm -r uberwriter/{pylocales,pressagio}
+  '';
+
+  preFixup = ''
+    gappsWrapperArgs+=(
+      --prefix PYTHONPATH : "$out/lib/python${pythonEnv.pythonVersion}/site-packages/"
+      --prefix PATH : "${texliveDist}/bin"
+      --prefix PATH : "${haskellPackages.pandoc-citeproc}/bin"
+    )
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = http://uberwriter.github.io/uberwriter/;
+    description = "A distraction free Markdown editor for GNU/Linux";
+    license = licenses.gpl3;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sternenseemann ];
+  };
+}
diff --git a/pkgs/applications/graphics/avocode/default.nix b/pkgs/applications/graphics/avocode/default.nix
@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   pname = "avocode";
-  version = "4.2.1";
+  version = "4.2.2";
 
   src = fetchurl {
     url = "https://media.avocode.com/download/avocode-app/${version}/avocode-${version}-linux.zip";
-    sha256 = "06g12gqri1sgfklla6jfpi7wm2qjazakcjs2w2rhrphnl50r6ca7";
+    sha256 = "0f4cmai2d1x7wbqllxp9na6gxgqfxqav8n4g9azyvm6ymd8zjnx8";
   };
 
   libPath = stdenv.lib.makeLibraryPath (with xorg; [

diff --git a/pkgs/applications/graphics/gthumb/default.nix b/pkgs/applications/graphics/gthumb/default.nix
@@ -33,11 +33,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gthumb";
-  version = "3.8.2";
+  version = "3.8.3";
 
   src = fetchurl {
     url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
-    sha256 = "15wqks35ks5dm7zj046dfd45vvrilan2ayfy2sxiprv7q74cip2q";
+    sha256 = "1a0gss9cjcwayrcpkam5kc1giwbfy38jgqxvh33in9gfq9dgrygg";
   };
 
   nativeBuildInputs = [

diff --git a/pkgs/applications/misc/calibre/default.nix b/pkgs/applications/misc/calibre/default.nix
@@ -1,7 +1,27 @@
-{ lib, mkDerivation, fetchurl, poppler_utils, pkgconfig, libpng
-, imagemagick, libjpeg, fontconfig, podofo, qtbase, qmake, icu, sqlite
-, unrarSupport ? false, chmlib, python2Packages, libusb1, libmtp
-, xdg_utils, makeDesktopItem, removeReferencesTo
+{ lib
+, mkDerivation
+, fetchurl
+, poppler_utils
+, pkgconfig
+, libpng
+, imagemagick
+, libjpeg
+, fontconfig
+, podofo
+, qtbase
+, qmake
+, icu
+, sqlite
+, hunspell
+, hyphen
+, unrarSupport ? false
+, chmlib
+, python2Packages
+, libusb1
+, libmtp
+, xdg_utils
+, makeDesktopItem
+, removeReferencesTo
 }:
 
 let
@@ -10,11 +30,11 @@ let
 in
 mkDerivation rec {
   pname = "calibre";
-  version = "3.48.0";
+  version = "4.8.0";
 
   src = fetchurl {
     url = "https://download.calibre-ebook.com/${version}/${pname}-${version}.tar.xz";
-    sha256 = "034m89h7j2088p324i1kya33dfldmqyynjxk3w98xiqkz7q2hi82";
+    sha256 = "1lk44qh3hzqhpz2b00iik7cgjg4xm36qjh2pxflkjnbk691gbpqk";
   };
 
   patches = [
@@ -44,17 +64,49 @@ mkDerivation rec {
   CALIBRE_PY3_PORT = builtins.toString pypkgs.isPy3k;
 
   buildInputs = [
-    poppler_utils libpng imagemagick libjpeg
-    fontconfig podofo qtbase chmlib icu sqlite libusb1 libmtp xdg_utils
-  ] ++ (with pypkgs; [
-    apsw cssselect css-parser dateutil dnspython feedparser html5-parser lxml markdown netifaces pillow
-    python pyqt5_with_qtwebkit sip
-    regex msgpack beautifulsoup4 html2text
-    # the following are distributed with calibre, but we use upstream instead
-    odfpy
-  ]) ++ lib.optionals (!pypkgs.isPy3k) (with pypkgs; [
-    mechanize
-  ]);
+    poppler_utils
+    libpng
+    imagemagick
+    libjpeg
+    fontconfig
+    podofo
+    qtbase
+    chmlib
+    icu
+    hunspell
+    hyphen
+    sqlite
+    libusb1
+    libmtp
+    xdg_utils
+  ] ++ (
+    with pypkgs; [
+      apsw
+      cssselect
+      css-parser
+      dateutil
+      dnspython
+      feedparser
+      html5-parser
+      lxml
+      markdown
+      netifaces
+      pillow
+      python
+      pyqt5_with_qtwebkit
+      sip
+      regex
+      msgpack
+      beautifulsoup4
+      html2text
+      # the following are distributed with calibre, but we use upstream instead
+      odfpy
+    ]
+  ) ++ lib.optionals (!pypkgs.isPy3k) (
+    with pypkgs; [
+      mechanize
+    ]
+  );
 
   installPhase = ''
     runHook preInstall