Merge staging-next into staging

34 files changed, 621 insertions, 378 deletions

diff --git a/pkgs/applications/misc/yubioath-desktop/default.nix b/pkgs/applications/misc/yubioath-desktop/default.nix
index 843bc0c1c234..d7a019c1c416 100644
--- a/pkgs/applications/misc/yubioath-desktop/default.nix
+++ b/pkgs/applications/misc/yubioath-desktop/default.nix
@@ -44,6 +44,7 @@ mkDerivation rec {
       cp resources/icons/*.{icns,ico,png,xpm} $out/share/yubioath/icons
       substituteInPlace $out/share/applications/yubioath-desktop.desktop \
         --replace 'Exec=yubioath-desktop' "Exec=$out/bin/yubioath-desktop" \
+        --replace 'Icon=yubioath' "Icon=$out/share/yubioath/icons/yubioath.png"
   '';
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/networking/flent/default.nix b/pkgs/applications/networking/flent/default.nix
index bc0a519a0eee..bbd9a7601acd 100644
--- a/pkgs/applications/networking/flent/default.nix
+++ b/pkgs/applications/networking/flent/default.nix
@@ -1,30 +1,39 @@
-{ stdenv, buildPythonApplication, fetchFromGitHub, matplotlib, procps, pyqt5
-, sphinx
-}:
+{ stdenv, buildPythonApplication, fetchPypi, matplotlib, procps, pyqt5, python
+, pythonPackages, qt5, sphinx, xvfb_run }:
 
 buildPythonApplication rec {
   pname = "flent";
-  version = "1.2.2";
-  src = fetchFromGitHub {
-    owner = "tohojo";
-    repo = "flent";
-    rev = "v${version}";
-    sha256 = "1llcdakk0nk9xlpjjz7mv4a80yq4sjnbqhaqvyj9m6lbcxgssh2r";
+  version = "1.3.0";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "099779i0ghjd9ikq77z6m6scnlmk946lw9issrgz8zm7babiw4d7";
   };
 
   buildInputs = [ sphinx ];
+  nativeBuildInputs = [ qt5.wrapQtAppsHook ];
+  propagatedBuildInputs = [ matplotlib procps pyqt5 ];
+  checkInputs = [ procps pythonPackages.mock pyqt5 xvfb_run ];
 
-  checkInputs = [ procps ];
+  checkPhase = ''
+    cat >test-runner <<EOF
+    #!/bin/sh
 
-  propagatedBuildInputs = [
-    matplotlib
-    procps
-    pyqt5
-  ];
+    ${python.pythonForBuild.interpreter} nix_run_setup test
+    EOF
+    chmod +x test-runner
+    wrapQtApp test-runner --prefix PYTHONPATH : $PYTHONPATH
+    xvfb-run -s '-screen 0 800x600x24' ./test-runner
+  '';
+
+  postInstall = ''
+    for program in $out/bin/*; do
+      wrapQtApp $program --prefix PYTHONPATH : $PYTHONPATH
+    done
+  '';
 
   meta = with stdenv.lib; {
     description = "The FLExible Network Tester";
-    homepage = https://flent.org;
+    homepage = "https://flent.org";
     license = licenses.gpl3;
 
     maintainers = [ maintainers.mmlb ];
diff --git a/pkgs/applications/networking/instant-messengers/discord/default.nix b/pkgs/applications/networking/instant-messengers/discord/default.nix
index 189092a6d5e0..1d9d645b0ed5 100644
--- a/pkgs/applications/networking/instant-messengers/discord/default.nix
+++ b/pkgs/applications/networking/instant-messengers/discord/default.nix
@@ -27,10 +27,10 @@ in {
     pname = "discord-canary";
     binaryName = "DiscordCanary";
     desktopName = "Discord Canary";
-    version = "0.0.93";
+    version = "0.0.95";
     src = fetchurl {
-      url = "https://dl-canary.discordapp.net/apps/linux/0.0.93/discord-canary-0.0.93.tar.gz";
-      sha256 = "1jzm5fm7a1p68ims7bv5am0bpbvrhbynzblpj9qrzzrwakdaywbi";
+      url = "https://dl-canary.discordapp.net/apps/linux/0.0.95/discord-canary-0.0.95.tar.gz";
+      sha256 = "06qhm73kc88pq0lgbi7qjy4gx9ighkmx128fdm1dpzfv62fjdasw";
     };
   };
 }.${branch}
diff --git a/pkgs/applications/networking/instant-messengers/mattermost-desktop/default.nix b/pkgs/applications/networking/instant-messengers/mattermost-desktop/default.nix
index 6f4e7e5b677b..f5f8414c870c 100644
--- a/pkgs/applications/networking/instant-messengers/mattermost-desktop/default.nix
+++ b/pkgs/applications/networking/instant-messengers/mattermost-desktop/default.nix
@@ -38,18 +38,18 @@ let
 in
   stdenv.mkDerivation rec {
     pname = "mattermost-desktop";
-    version = "4.2.0";
+    version = "4.2.3";
 
     src =
       if stdenv.hostPlatform.system == "x86_64-linux" then
         fetchurl {
           url = "https://releases.mattermost.com/desktop/${version}/${pname}-${version}-linux-x64.tar.gz";
-          sha256 = "0hka94gwpscjn61032c0grpjv5gjb0j8rkx6pgwci617n29xkyf6";
+          sha256 = "14xyn8dp0xxl4j9xdsjik9p6srqdxbirgcgym2sv64p01w3kc9wf";
         }
       else if stdenv.hostPlatform.system == "i686-linux" then
         fetchurl {
           url = "https://releases.mattermost.com/desktop/${version}/${pname}-${version}-linux-ia32.tar.gz";
-          sha256 = "1nx2sgbnr60h6kn56wv54m7cvyx27d64bfprpb94hqd5c2z21x80";
+          sha256 = "063rrxw76mjz71wp9xd3ppkq3s017vrzms879r2cilypmay7fhgs";
         }
       else
         throw "Mattermost-Desktop is not currently supported on ${stdenv.hostPlatform.system}";
diff --git a/pkgs/applications/networking/remote/x2goserver/default.nix b/pkgs/applications/networking/remote/x2goserver/default.nix
new file mode 100644
index 000000000000..f69d2326217d
--- /dev/null
+++ b/pkgs/applications/networking/remote/x2goserver/default.nix
@@ -0,0 +1,93 @@
+{ stdenv, lib, fetchurl, perlPackages, makeWrapper, perl, which, nx-libs
+, utillinux, coreutils, glibc, gawk, gnused, gnugrep, findutils, xorg
+, nettools, iproute, bc, procps, psmisc, lsof, pwgen, openssh, sshfs, bash
+}:
+
+let
+  pname = "x2goserver";
+  version = "4.1.0.3";
+
+  src = fetchurl {
+    url = "http://code.x2go.org/releases/source/x2goserver/${pname}-${version}.tar.gz";
+    sha256 = "1l6wd708kbipib4ldprfiihqmj4895nifg0bkws4x97majislxk7";
+  };
+
+  x2go-perl = perlPackages.buildPerlPackage rec {
+    pname = "X2Go";
+    inherit version src;
+    makeFlags = [ "-f" "Makefile.perl" ];
+    patchPhase = ''
+      substituteInPlace X2Go/Config.pm --replace '/etc/x2go' '/var/lib/x2go/conf'
+      substituteInPlace X2Go/Server/DB.pm \
+        --replace '$x2go_lib_path/libx2go-server-db-sqlite3-wrapper' \
+                  '/run/wrappers/bin/x2gosqliteWrapper'
+      substituteInPlace X2Go/Server/DB/SQLite3.pm --replace "user='x2gouser'" "user='x2go'"
+    '';
+  };
+
+  perlEnv = perl.withPackages (p: with p; [
+    x2go-perl DBI DBDSQLite FileBaseDir TryTiny CaptureTiny ConfigSimple Switch
+  ]);
+
+  binaryDeps = [
+    perlEnv which nx-libs utillinux coreutils glibc.bin gawk gnused gnugrep
+    findutils nettools iproute bc procps psmisc lsof pwgen openssh sshfs
+    xorg.xauth xorg.xinit xorg.xrandr xorg.xmodmap xorg.xwininfo xorg.fontutil
+    xorg.xkbcomp xorg.setxkbmap
+  ];
+in
+stdenv.mkDerivation rec {
+  inherit pname version src;
+
+  buildInputs = [ perlEnv bash ];
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  prePatch = ''
+    patchShebangs .
+    sed -i '/Makefile.PL\|Makefile.perl/d' Makefile
+    for i in */Makefile; do
+      substituteInPlace "$i" --replace "-o root -g root " ""
+    done
+    substituteInPlace libx2go-server-db-perl/Makefile --replace "chmod 2755" "chmod 755"
+    for i in x2goserver/sbin/x2godbadmin x2goserver/bin/x2go*
+    do
+      substituteInPlace $i --replace '/etc/x2go' '/var/lib/x2go/conf'
+    done
+    substituteInPlace x2goserver/sbin/x2gocleansessions \
+      --replace '/var/run/x2goserver.pid' '/var/run/x2go/x2goserver.pid'
+    substituteInPlace x2goserver/sbin/x2godbadmin --replace 'user="x2gouser"' 'user="x2go"'
+    substituteInPlace x2goserver-xsession/etc/Xsession \
+      --replace "SSH_AGENT /bin/bash -c" "SSH_AGENT ${bash}/bin/bash -c" \
+      --replace "[ -f /etc/redhat-release ]" "[ -d /etc/nix ] || [ -f /etc/redhat-release ]"
+  '';
+
+  makeFlags = [ "PREFIX=/" "NXLIBDIR=${nx-libs}/lib/nx" ];
+
+  installFlags = [ "DESTDIR=$(out)" ];
+
+  postInstall = ''
+    mv $out/etc/x2go/x2goserver.conf{,.example}
+    mv $out/etc/x2go/x2goagent.options{,.example}
+    ln -sf ${nx-libs}/bin/nxagent $out/bin/x2goagent
+    for i in $out/sbin/x2go* $(find $out/bin -type f) \
+      $(ls $out/lib/x2go/x2go* | grep -v x2gocheckport)
+    do
+      wrapProgram $i --prefix PATH : ${lib.makeBinPath binaryDeps}:$out
+    done
+    # We're patching @INC of the setgid wrapper, because we can't mix
+    # the perl wrapper (for PERL5LIB) with security.wrappers (for setgid)
+    sed -ie "s,.\+bin/perl,#!${perl}/bin/perl -I ${perlEnv}/lib/perl5/site_perl," \
+      $out/lib/x2go/libx2go-server-db-sqlite3-wrapper.pl
+  '';
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    description = "Remote desktop application, server component";
+    homepage = "http://x2go.org/";
+    platforms = stdenv.lib.platforms.linux;
+    license = licenses.gpl2;
+    maintainers = [ maintainers.averelld ];
+  };
+}
diff --git a/pkgs/applications/science/biology/trimal/default.nix b/pkgs/applications/science/biology/trimal/default.nix
new file mode 100755
index 000000000000..d4e8fee7bc36
--- /dev/null
+++ b/pkgs/applications/science/biology/trimal/default.nix
@@ -0,0 +1,31 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  pname = "trimal";
+  version = "1.4.1";
+
+  src = fetchFromGitHub {
+    repo = pname;
+    owner = "scapella";
+    rev = "v${version}";
+    sha256 = "0isc7s3514di4z953xq53ncjkbi650sh4q9yyw5aag1n9hqnh7k0";
+  };
+
+  postUnpack = ''
+    sourceRoot=''${sourceRoot}/source
+    echo Source root reset to ''${sourceRoot}
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp -a trimal readal statal $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment";
+    license = licenses.gpl3;
+    platforms = platforms.linux;
+    homepage = http://trimal.cgenomics.org;
+    maintainers = [ maintainers.bzizou ];
+  };
+}
diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix
index 72827112c50c..89ae354e7c76 100644
--- a/pkgs/applications/science/math/pari/default.nix
+++ b/pkgs/applications/science/math/pari/default.nix
@@ -1,6 +1,5 @@
 { stdenv
 , fetchurl
-, fetchpatch
 , gmp
 , readline
 , libX11
@@ -13,25 +12,13 @@ assert withThread -> libpthreadstubs != null;
 
 stdenv.mkDerivation rec {
   pname = "pari";
-  version = "2.11.1";
+  version = "2.11.2";
 
   src = fetchurl {
     url = "https://pari.math.u-bordeaux.fr/pub/pari/unix/${pname}-${version}.tar.gz";
-    sha256 = "1jfax92jpydjd02fwl30r6b8kfzqqd6sm4yx94gidyz9lqjb7a94";
+    sha256 = "0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa";
   };
 
-  patches = [
-    # Fix a off-by-one bug that can potentially lead to segfaults (accepted upstream)
-    # https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2117
-    # https://trac.sagemath.org/ticket/27335
-    (fetchpatch {
-      name = "fix-off-by-one-error.patch";
-      # only relevant parts of https://pari.math.u-bordeaux.fr/cgi-bin/gitweb.cgi?p=pari.git;a=patch;h=aa1ee6e0898d177e6bcf49237d82c804bc410985
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pari/patches/red_montgomery.patch?id=bbea55c96e1f05302b3c7f593cf64492497047c5";
-      sha256 = "0vqkmhgv9splsdswp6zjnkj50z76rc1m6k9iy3cf9dxwqw3h3nr6";
-    })
-  ];
-
   buildInputs = [
     gmp
     readline
diff --git a/pkgs/applications/science/misc/colmap/default.nix b/pkgs/applications/science/misc/colmap/default.nix
new file mode 100644
index 000000000000..672569ed1002
--- /dev/null
+++ b/pkgs/applications/science/misc/colmap/default.nix
@@ -0,0 +1,37 @@
+{ mkDerivation, lib, fetchFromGitHub, cmake, boost, ceres-solver, eigen,
+  freeimage, glog, libGLU, glew, qtbase,
+  cudaSupport ? false, cudatoolkit ? null }:
+
+assert !cudaSupport || cudatoolkit != null;
+
+let boost_static = boost.override { enableStatic = true; };
+in 
+mkDerivation rec {
+  version = "3.5";
+  pname = "colmap";
+  src = fetchFromGitHub {
+     owner = "colmap";
+     repo = "colmap";
+     rev = version;
+     sha256 = "1vnb62p0y2bnga173wmjs0lnyqdjikv0fkcxjzxm8187khk2lly8";
+  };
+  
+  buildInputs = [
+    boost_static ceres-solver eigen
+    freeimage glog libGLU glew qtbase
+  ] ++ lib.optional cudaSupport cudatoolkit;
+
+  nativeBuildInputs = [ cmake ];
+
+  meta = with lib; {
+    description = "COLMAP - Structure-From-Motion and Multi-View Stereo pipeline";
+    longDescription = ''
+       COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline
+       with a graphical and command-line interface.
+    '';
+    homepage = https://colmap.github.io/index.html;
+    license = licenses.bsd2;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ lebastr ];
+  };
+}
diff --git a/pkgs/development/compilers/glslang/default.nix b/pkgs/development/compilers/glslang/default.nix
index 79ad90e77a6e..161e57b54792 100644
--- a/pkgs/development/compilers/glslang/default.nix
+++ b/pkgs/development/compilers/glslang/default.nix
@@ -1,16 +1,29 @@
-{ stdenv, fetchFromGitHub, cmake, bison, jq, python, spirv-tools, spirv-headers }:
+{ stdenv, fetchFromGitHub
+, bison
+, cmake
+, jq
+, python3
+, spirv-headers
+, spirv-tools
+}:
+
 stdenv.mkDerivation rec {
   pname = "glslang";
-  version = "7.11.3113";
+  version = "7.11.3214";
 
   src = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "glslang";
-    rev = "${version}";
-    sha256 = "1kzv2b4q1fddxd7c0hc754nd6rw6y9vijb9fsi13xzzq9dficgb6";
+    rev = version;
+    sha256 = "0dqjga0lcza006fhac26zp2plbq4gx8a6nsmrwkqlzji6lw1jins";
+  };
+
+  # These get set at all-packages, keep onto them for child drvs
+  passthru = {
+    inherit spirv-tools spirv-headers;
   };
 
-  nativeBuildInputs = [ cmake python bison jq ];
+  nativeBuildInputs = [ cmake python3 bison jq ];
   enableParallelBuilding = true;
 
   postPatch = ''
@@ -18,6 +31,7 @@ stdenv.mkDerivation rec {
     ln -s "${spirv-headers.src}" External/spirv-tools/external/spirv-headers
   '';
 
+  # Ensure spirv-headers and spirv-tools match exactly to what is expected
   preConfigure = ''
     HEADERS_COMMIT=$(jq -r < known_good.json '.commits|map(select(.name=="spirv-tools/external/spirv-headers"))[0].commit')
     TOOLS_COMMIT=$(jq -r < known_good.json '.commits|map(select(.name=="spirv-tools"))[0].commit')
diff --git a/pkgs/development/libraries/opencv/3.x.nix b/pkgs/development/libraries/opencv/3.x.nix
index d7f897ebcf83..d8946dae095b 100644
--- a/pkgs/development/libraries/opencv/3.x.nix
+++ b/pkgs/development/libraries/opencv/3.x.nix
@@ -14,7 +14,8 @@
 , enableOpenblas  ? true, openblas
 , enableContrib   ? true
 
-, enableCuda      ? config.cudaSupport or false, cudatoolkit
+, enableCuda      ? (config.cudaSupport or false) &&
+                    stdenv.hostPlatform.isx86_64, cudatoolkit
 
 , enableUnfree    ? false
 , enableIpp       ? false
diff --git a/pkgs/development/libraries/opencv/4.x.nix b/pkgs/development/libraries/opencv/4.x.nix
index 153737e2761e..aa4c7afa4dbe 100644
--- a/pkgs/development/libraries/opencv/4.x.nix
+++ b/pkgs/development/libraries/opencv/4.x.nix
@@ -14,7 +14,8 @@
 , enableOpenblas  ? true, openblas
 , enableContrib   ? true
 
-, enableCuda      ? config.cudaSupport or false, cudatoolkit
+, enableCuda      ? (config.cudaSupport or false) &&
+                    stdenv.hostPlatform.isx86_64, cudatoolkit
 
 , enableUnfree    ? false
 , enableIpp       ? false
diff --git a/pkgs/development/libraries/spirv-headers/default.nix b/pkgs/development/libraries/spirv-headers/default.nix
index 98c8ced5b47a..9b2c0032d4e9 100644
--- a/pkgs/development/libraries/spirv-headers/default.nix
+++ b/pkgs/development/libraries/spirv-headers/default.nix
@@ -1,13 +1,14 @@
 { stdenv, fetchFromGitHub, cmake }:
+
 stdenv.mkDerivation rec {
   pname = "spirv-headers";
-  version = "2019.1"; # spirv-tools version whose DEPS file calls for this commit
+  version = "1.4.1";
 
   src = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "SPIRV-Headers";
-    rev = "79b6681aadcb53c27d1052e5f8a0e82a981dbf2f"; # from spirv-tools' DEPS
-    sha256 = "0flng2rdmc4ndq3j71h6wk1ibcjvhjrg2rzd6rv445vcsf0jh2pj";
+    rev = version;
+    sha256 = "1zfmvg3x0q9w652s8g5m5rcckzm6jiiw8rif2qck4vlsryl55akp";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/development/libraries/vulkan-headers/default.nix b/pkgs/development/libraries/vulkan-headers/default.nix
index de233b49f3aa..032181e458ea 100644
--- a/pkgs/development/libraries/vulkan-headers/default.nix
+++ b/pkgs/development/libraries/vulkan-headers/default.nix
@@ -3,13 +3,13 @@ stdenv.mkDerivation rec {
   pname = "vulkan-headers";
   version = "1.1.106";
 
-  buildInputs = [ cmake ];
+  nativeBuildInputs = [ cmake ];
 
   src = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "Vulkan-Headers";
     rev = "sdk-${version}";
-    sha256 = "0idw7q715ikj575qmspvgq2gzc6c1sj581b8z3xnv6wz9qbzrmsd";
+    sha256 = "0fdvh26nxibylh32lj8b62d9nf9j25xa0il9zg362wmr2zgm8gka";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/vulkan-loader/default.nix b/pkgs/development/libraries/vulkan-loader/default.nix
index 5bb3788a3b47..3cdf8f08651f 100644
--- a/pkgs/development/libraries/vulkan-loader/default.nix
+++ b/pkgs/development/libraries/vulkan-loader/default.nix
@@ -2,7 +2,7 @@
 , xlibsWrapper, libxcb, libXrandr, libXext, wayland, addOpenGLRunpath }:
 
 let
-  version = "1.1.106";
+  version = "1.1.114.0";
 in
 
 assert version == vulkan-headers.version;
@@ -14,17 +14,15 @@ stdenv.mkDerivation {
     owner = "KhronosGroup";
     repo = "Vulkan-Loader";
     rev = "sdk-${version}";
-    sha256 = "0zhrwj1gi90x2w8gaaaw5h4b969a8gfy244kn0drrplhhb1nqz3b";
+    sha256 = "08nibkbjf3g32qyp5bpdvj7i0zdv5ds1n5y52z8pvyzkpiz7s6ww";
   };
 
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ cmake python3 xlibsWrapper libxcb libXrandr libXext wayland ];
   enableParallelBuilding = true;
 
-  patches = [ ./system-search-path.patch ];
-
   cmakeFlags = [
-    "-DSYSTEM_SEARCH_PATH=${addOpenGLRunpath.driverLink}/share"
+    "-DSYSCONFDIR=${addOpenGLRunpath.driverLink}/share"
     "-DVULKAN_HEADERS_INSTALL_DIR=${vulkan-headers}"
   ];
 
diff --git a/pkgs/development/libraries/vulkan-loader/system-search-path.patch b/pkgs/development/libraries/vulkan-loader/system-search-path.patch
deleted file mode 100644
index 26f83e6d534f..000000000000
--- a/pkgs/development/libraries/vulkan-loader/system-search-path.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 9ac5ce835..cbdb0ff56 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -88,6 +88,12 @@ if(UNIX)
-             STRING
-             "Search path to use when XDG_DATA_DIRS is unset or empty or the current process is SUID/SGID. Default is freedesktop compliant."
-         )
-+    set(
-+        SYSTEM_SEARCH_PATH ""
-+        CACHE
-+            STRING
-+            "Search path to always use, after all other search paths."
-+    )
- endif()
- 
- if(UNIX AND NOT APPLE) # i.e.: Linux
-@@ -184,6 +190,7 @@ if(UNIX)
-     add_definitions(-DFALLBACK_CONFIG_DIRS="${FALLBACK_CONFIG_DIRS}")
-     add_definitions(-DFALLBACK_DATA_DIRS="${FALLBACK_DATA_DIRS}")
-     add_definitions(-DSYSCONFDIR="${CMAKE_INSTALL_FULL_SYSCONFDIR}")
-+    add_definitions(-DSYSTEM_SEARCH_PATH="${SYSTEM_SEARCH_PATH}")
- 
-     # Make sure /etc is searched by the loader
-     if(NOT (CMAKE_INSTALL_FULL_SYSCONFDIR STREQUAL "/etc"))
-diff --git a/loader/loader.c b/loader/loader.c
-index 0d3b5a947..abe357004 100644
---- a/loader/loader.c
-+++ b/loader/loader.c
-@@ -3688,6 +3688,7 @@ static VkResult ReadDataFilesInSearchPaths(const struct loader_instance *inst, e
-                 search_path_size += DetermineDataFilePathSize(xdgdatahome, rel_size);
-                 search_path_size += DetermineDataFilePathSize(home_root, rel_size);
-             }
-+            search_path_size += DetermineDataFilePathSize(SYSTEM_SEARCH_PATH, rel_size);
- #endif
-         }
-     }
-@@ -3737,6 +3738,7 @@ static VkResult ReadDataFilesInSearchPaths(const struct loader_instance *inst, e
-                 CopyDataFilePath(xdgdatahome, relative_location, rel_size, &cur_path_ptr);
-                 CopyDataFilePath(home_root, relative_location, rel_size, &cur_path_ptr);
-             }
-+            CopyDataFilePath(SYSTEM_SEARCH_PATH, relative_location, rel_size, &cur_path_ptr);
-         }
- 
-         // Remove the last path separator
diff --git a/pkgs/development/mobile/cocoapods/Gemfile-beta.lock b/pkgs/development/mobile/cocoapods/Gemfile-beta.lock
index 2ddffbf16b7c..c75dc334ebc9 100644
--- a/pkgs/development/mobile/cocoapods/Gemfile-beta.lock
+++ b/pkgs/development/mobile/cocoapods/Gemfile-beta.lock
@@ -1,7 +1,7 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    CFPropertyList (3.0.0)
+    CFPropertyList (3.0.1)
     activesupport (4.2.11.1)
       i18n (~> 0.7)
       minitest (~> 5.1)
@@ -12,16 +12,16 @@ GEM
       json (>= 1.5.1)
     atomos (0.1.3)
     claide (1.0.3)
-    cocoapods (1.8.0.beta.1)
+    cocoapods (1.8.0.beta.2)
       activesupport (>= 4.0.2, < 5)
       claide (>= 1.0.2, < 2.0)
-      cocoapods-core (= 1.8.0.beta.1)
+      cocoapods-core (= 1.8.0.beta.2)
       cocoapods-deintegrate (>= 1.0.3, < 2.0)
       cocoapods-downloader (>= 1.2.2, < 2.0)
       cocoapods-plugins (>= 1.0.0, < 2.0)
       cocoapods-search (>= 1.0.0, < 2.0)
       cocoapods-stats (>= 1.0.0, < 2.0)
-      cocoapods-trunk (>= 1.3.1, < 2.0)
+      cocoapods-trunk (>= 1.4.0, < 2.0)
       cocoapods-try (>= 1.1.0, < 2.0)
       colored2 (~> 3.1)
       escape (~> 0.0.4)
@@ -31,9 +31,10 @@ GEM
       nap (~> 1.0)
       ruby-macho (~> 1.4)
       xcodeproj (>= 1.11.1, < 2.0)
-    cocoapods-core (1.8.0.beta.1)
+    cocoapods-core (1.8.0.beta.2)
       activesupport (>= 4.0.2, < 6)
       algoliasearch (~> 1.0)
+      concurrent-ruby (~> 1.0)
       fuzzy_match (~> 2.0.4)
       nap (~> 1.0)
     cocoapods-deintegrate (1.0.4)
@@ -42,7 +43,7 @@ GEM
       nap
     cocoapods-search (1.0.0)
     cocoapods-stats (1.1.0)
-    cocoapods-trunk (1.3.1)
+    cocoapods-trunk (1.4.0)
       nap (>= 0.8, < 2.0)
       netrc (~> 0.11)
     cocoapods-try (1.1.0)
diff --git a/pkgs/development/mobile/cocoapods/gemset-beta.nix b/pkgs/development/mobile/cocoapods/gemset-beta.nix
index baa4748fb946..e2d4127ae44d 100644
--- a/pkgs/development/mobile/cocoapods/gemset-beta.nix
+++ b/pkgs/development/mobile/cocoapods/gemset-beta.nix
@@ -36,10 +36,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0ykjag3k5msz3sf1j91rb55da2xh596y06m3a4yl79fiy2id0w9z";
+      sha256 = "0fr8sdzs2q1969zqh790w223hjidlwx4hfm4c91gj0va5j5pv3n8";
       type = "gem";
     };
-    version = "3.0.0";
+    version = "3.0.1";
   };
   claide = {
     groups = ["default"];
@@ -57,21 +57,21 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1gs9ybf1zbajhsn591dwh2papj0bs1dzbnw8shbsm4mfqz976y54";
+      sha256 = "1qsj34czqsy93w2bnwhdhr0cyzjwl7vy3sknmak4syyni6m0rlli";
       type = "gem";
     };
-    version = "1.8.0.beta.1";
+    version = "1.8.0.beta.2";
   };
   cocoapods-core = {
-    dependencies = ["activesupport" "algoliasearch" "fuzzy_match" "nap"];
+    dependencies = ["activesupport" "algoliasearch" "concurrent-ruby" "fuzzy_match" "nap"];
     groups = ["default"];
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "02c0415b7iridf0gypajm4i3vqpq8zs6vx8bw49rm70l554jp14j";
+      sha256 = "166pr9m3da9hsra9rviaxz3i4spm7kl003mkn7sn25r9smcvfdj4";
       type = "gem";
     };
-    version = "1.8.0.beta.1";
+    version = "1.8.0.beta.2";
   };
   cocoapods-deintegrate = {
     groups = ["default"];
@@ -130,10 +130,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1plssgabdv6hcaq1c3gf43kf1d2prx883q8lzdr6chi5byzzs3yl";
+      sha256 = "1m0p27aij7d0n0b8h7nvyv3q3prcpwisbj7sla0fp2hvn4lqarl5";
       type = "gem";
     };
-    version = "1.3.1";
+    version = "1.4.0";
   };
   cocoapods-try = {
     groups = ["default"];
diff --git a/pkgs/development/python-modules/mailman-hyperkitty/default.nix b/pkgs/development/python-modules/mailman-hyperkitty/default.nix
new file mode 100644
index 000000000000..fd89260ab94b
--- /dev/null
+++ b/