treewide(java-users): clean callPackage overrides, by-name some

**This commit should cause no rebuilds.**

# Moving Java overrides out of all-packages

All usages of this pattern have been moved to
'let ... in' blocks.

Patterns I searched for:
* `jdk =`
* `jdk_headless =`
* `jre =`
* `jfx =`

The `jing` alias has been moved to aliases.nix, so
update the usage of `jing` in `xmloscopy` to
`jing-trang`.

cassandra was ignored because that derivation
involves code generation.

I ignored grails, because jdk is set to null by
default by an override in all-packages.nix. That
package would need a slightly larger refactor to
deal with.

Packages with a *-native variant were ignored because
those would need to be refactored.

jetbrains was ignored because that might be a special case?

I ignored virtualbox, because I did not want
to touch the usages of the pattern for other
dependencies.

pkgs/applications/editors/greenfoot/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchurl,
-  openjdk,
-  glib,
-  dpkg,
-  wrapGAppsHook3,
-}:
-
-stdenv.mkDerivation rec {
-  pname = "greenfoot";
-  version = "3.9.0";
-
-  src = fetchurl {
-    # We use the deb here. First instinct might be to go for the "generic" JAR
-    # download, but that is actually a graphical installer that is much harder
-    # to unpack than the deb.
-    url = "https://www.greenfoot.org/download/files/Greenfoot-linux-arm64-${
-      builtins.replaceStrings [ "." ] [ "" ] version
-    }.deb";
-    hash = "sha256-d5bkK+teTA4fxFb46ovbZE28l8WILGStv3Vg3nJZfv0=";
-  };
-
-  nativeBuildInputs = [
-    dpkg
-    wrapGAppsHook3
-  ];
-  buildInputs = [ glib ];
-
-  dontWrapGApps = true;
-
-  installPhase = ''
-    runHook preInstall
-
-    mkdir -p $out
-    cp -r usr/* $out
-
-    rm -r $out/share/greenfoot/jdk
-    rm -r $out/share/greenfoot/javafx-*.jar
-
-    makeWrapper ${openjdk}/bin/java $out/bin/greenfoot \
-      "''${gappsWrapperArgs[@]}" \
-      --add-flags "-Dawt.useSystemAAFontSettings=gasp -Xmx512M \
-                   --add-opens javafx.graphics/com.sun.glass.ui=ALL-UNNAMED \
-                   -cp $out/share/greenfoot/boot.jar bluej.Boot \
-                   -greenfoot=true -bluej.compiler.showunchecked=false \
-                   -greenfoot.scenarios=$out/share/doc/Greenfoot/scenarios \
-                   -greenfoot.url.javadoc=file://$out/share/doc/Greenfoot/API"
-
-    runHook postInstall
-  '';
-
-  meta = with lib; {
-    description = "Simple integrated development environment for Java";
-    homepage = "https://www.greenfoot.org/";
-    sourceProvenance = with sourceTypes; [ binaryBytecode ];
-    license = with licenses; [
-      gpl2Plus
-      classpathException20
-    ];
-    mainProgram = "greenfoot";
-    maintainers = [ maintainers.chvp ];
-    platforms = platforms.linux;
-  };
-}

pkgs/applications/graphics/processing/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  fetchurl,
-  ant,
-  unzip,
-  makeWrapper,
-  jdk,
-  jogl,
-  rsync,
-  ffmpeg,
-  batik,
-  stripJavaArchivesHook,
-  wrapGAppsHook3,
-  libGL,
-}:
-let
-  buildNumber = "1295";
-  vaqua = fetchurl {
-    name = "VAqua9.jar";
-    url = "https://violetlib.org/release/vaqua/9/VAqua9.jar";
-    sha256 = "cd0b82df8e7434c902ec873364bf3e9a3e6bef8b59cbf42433130d71bf1a779c";
-  };
-
-  jna = fetchurl {
-    name = "jna-5.10.0.zip";
-    url = "https://github.com/java-native-access/jna/archive/5.10.0.zip";
-    sha256 = "B5CakOQ8225xNsk2TMV8CbK3RcsLlb+pHzjaY5JNwg0=";
-  };
-
-  flatlaf = fetchurl {
-    name = "flatlaf-2.4.jar";
-    url = "mirror://maven/com/formdev/flatlaf/2.4/flatlaf-2.4.jar";
-    sha256 = "NVMYiCd+koNCJ6X3EiRx1Aj+T5uAMSJ9juMmB5Os+zc=";
-  };
-
-  lsp4j = fetchurl {
-    name = "org.eclipse.lsp4j-0.19.0.jar";
-    url = "mirror://maven/org/eclipse/lsp4j/org.eclipse.lsp4j/0.19.0/org.eclipse.lsp4j-0.19.0.jar";
-    sha256 = "sha256-1DI5D9KW+GL4gT1qjwVZveOl5KVOEjt6uXDwsFzi8Sg=";
-  };
-
-  lsp4j-jsonrpc = fetchurl {
-    name = "org.eclipse.lsp4j.jsonrpc-0.19.0.jar";
-    url = "mirror://maven/org/eclipse/lsp4j/org.eclipse.lsp4j.jsonrpc/0.19.0/org.eclipse.lsp4j.jsonrpc-0.19.0.jar";
-    sha256 = "sha256-ozYTkvv7k0psCeX/PbSM3/Bl17qT3upX3trt65lmM9I=";
-  };
-
-  gson = fetchurl {
-    name = "gson-2.9.1.jar";
-    url = "mirror://maven/com/google/code/gson/gson/2.9.1/gson-2.9.1.jar";
-    sha256 = "sha256-N4U04znm5tULFzb7Ort28cFdG+P0wTzsbVNkEuI9pgM=";
-  };
-
-  arch =
-    {
-      x86_64 = "amd64";
-    }
-    .${stdenv.hostPlatform.parsed.cpu.name} or stdenv.hostPlatform.parsed.cpu.name;
-in
-stdenv.mkDerivation rec {
-  pname = "processing";
-  version = "4.3.2";
-
-  src = fetchFromGitHub {
-    owner = "processing";
-    repo = "processing4";
-    rev = "processing-${buildNumber}-${version}";
-    sha256 = "sha256-jUkWnkP8up5vpaXfgFJ/jQjN1KfeX5EuYXSb+W6NEms=";
-  };
-
-  # Processing did not update the todo.txt file before tagging this release, so
-  # the "revision-check" Ant target fails.
-  patches = [ ./disable-revision-check.patch ];
-
-  nativeBuildInputs = [
-    ant
-    unzip
-    makeWrapper
-    stripJavaArchivesHook
-    wrapGAppsHook3
-  ];
-  buildInputs = [
-    jdk
-    jogl
-    ant
-    rsync
-    ffmpeg
-    batik
-  ];
-
-  dontWrapGApps = true;
-
-  buildPhase = ''
-    runHook preBuild
-
-    echo "tarring jdk"
-    tar --checkpoint=10000 -czf build/linux/jdk-17.0.8-${arch}.tgz ${jdk}
-    cp ${ant.home}/lib/{ant.jar,ant-launcher.jar} app/lib/
-    mkdir -p core/library
-    ln -s ${jogl}/share/java/* core/library/
-    ln -s ${vaqua} app/lib/VAqua9.jar
-    ln -s ${flatlaf} app/lib/flatlaf.jar
-    ln -s ${lsp4j} java/mode/org.eclipse.lsp4j.jar
-    ln -s ${lsp4j-jsonrpc} java/mode/org.eclipse.lsp4j.jsonrpc.jar
-    ln -s ${gson} java/mode/gson.jar
-    unzip -qo ${jna} -d app/lib/
-    mv app/lib/{jna-5.10.0/dist/jna.jar,}
-    mv app/lib/{jna-5.10.0/dist/jna-platform.jar,}
-    ln -sf ${batik}/* java/libraries/svg/library/
-    cp java/libraries/svg/library/share/java/batik-all-${batik.version}.jar java/libraries/svg/library/batik.jar
-    echo "tarring ffmpeg"
-    tar --checkpoint=10000 -czf build/shared/tools/MovieMaker/ffmpeg-5.0.1.gz ${ffmpeg}
-    cd build
-    ant build
-    cd ..
-
-    runHook postBuild
-  '';
-
-  installPhase = ''
-    runHook preInstall
-
-    mkdir -p $out/share/
-    mkdir -p $out/share/applications/
-    cp -dp build/linux/${pname}.desktop $out/share/applications/
-    cp -dpr build/linux/work $out/share/${pname}
-    rmdir $out/share/${pname}/java
-    ln -s ${jdk} $out/share/${pname}/java
-    makeWrapper $out/share/${pname}/processing $out/bin/processing \
-      ''${gappsWrapperArgs[@]} \
-      --prefix LD_LIBRARY_PATH : "${lib.makeLibraryPath [ libGL ]}" \
-      --prefix _JAVA_OPTIONS " " "-Dawt.useSystemAAFontSettings=gasp"
-    makeWrapper $out/share/${pname}/processing-java $out/bin/processing-java \
-      ''${gappsWrapperArgs[@]} \
-      --prefix LD_LIBRARY_PATH : "${lib.makeLibraryPath [ libGL ]}" \
-      --prefix _JAVA_OPTIONS " " "-Dawt.useSystemAAFontSettings=gasp"
-
-    runHook postInstall
-  '';
-
-  meta = with lib; {
-    description = "Language and IDE for electronic arts";
-    homepage = "https://processing.org";
-    license = with licenses; [
-      gpl2Only
-      lgpl21Only
-    ];
-    platforms = platforms.linux;
-    maintainers = with maintainers; [ evan-goode ];
-  };
-}

pkgs/applications/misc/ganttproject-bin/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchzip,
-  makeDesktopItem,
-  makeWrapper,
-  jre,
-}:
-
-stdenv.mkDerivation rec {
-  pname = "ganttproject-bin";
-  version = "3.3.3316";
-
-  src = fetchzip {
-    url = "https://dl.ganttproject.biz/ganttproject-${version}/ganttproject-${version}.zip";
-    stripRoot = false;
-    hash = "sha256-tiEq/xdC0gXiUInLS9xGR/vI/BpdSA+mSf5yukuejc4=";
-  };
-
-  nativeBuildInputs = [ makeWrapper ];
-  buildInputs = [ jre ];
-
-  installPhase =
-    let
-
-      desktopItem = makeDesktopItem {
-        name = "ganttproject";
-        exec = "ganttproject";
-        icon = "ganttproject";
-        desktopName = "GanttProject";
-        genericName = "Shedule and manage projects";
-        comment = meta.description;
-        categories = [ "Office" ];
-      };
-
-      javaOptions = [
-        "-Dawt.useSystemAAFontSettings=gasp"
-      ];
-
-    in
-    ''
-      mkdir -pv "$out/share/ganttproject"
-      cp -rv *  "$out/share/ganttproject"
-
-      mkdir -pv "$out/bin"
-      wrapProgram "$out/share/ganttproject/ganttproject" \
-        --set JAVA_HOME "${jre}" \
-        --prefix _JAVA_OPTIONS " " "${builtins.toString javaOptions}"
-
-      mv -v "$out/share/ganttproject/ganttproject" "$out/bin"
-
-      cp -rv "${desktopItem}/share/applications" "$out/share"
-    '';
-
-  meta = with lib; {
-    description = "Project scheduling and management";
-    homepage = "https://www.ganttproject.biz/";
-    downloadPage = "https://www.ganttproject.biz/download";
-    # GanttProject itself is GPL3+. All bundled libraries are declared
-    # ‘GPL3-compatible’. See ${downloadPage} for detailed information.
-    license = licenses.gpl3Plus;
-    platforms = platforms.linux;
-    maintainers = [ maintainers.vidbina ];
-    mainProgram = "ganttproject";
-  };
-}

pkgs/applications/misc/gremlin-console/default.nix

···
-{
-  fetchzip,
-  lib,
-  stdenv,
-  makeWrapper,
-  openjdk,
-}:
-
-stdenv.mkDerivation rec {
-  pname = "gremlin-console";
-  version = "3.7.4";
-  src = fetchzip {
-    url = "https://downloads.apache.org/tinkerpop/${version}/apache-tinkerpop-gremlin-console-${version}-bin.zip";
-    sha256 = "sha256-Z971M4W359WKs2NjLeWej5IVHnFu5LLsffxl0jraB60=";
-  };
-
-  nativeBuildInputs = [ makeWrapper ];
-
-  installPhase = ''
-    runHook preInstall
-    mkdir -p $out/opt
-    cp -r ext lib $out/opt/
-    install -D bin/gremlin.sh $out/opt/bin/gremlin-console
-    makeWrapper $out/opt/bin/gremlin-console $out/bin/gremlin-console \
-      --prefix PATH ":" "${openjdk}/bin/" \
-      --set CLASSPATH "$out/opt/lib/"
-    runHook postInstall
-  '';
-
-  meta = with lib; {
-    homepage = "https://tinkerpop.apache.org/";
-    description = "Console of the Apache TinkerPop graph computing framework";
-    license = licenses.asl20;
-    maintainers = [ maintainers.lewo ];
-    platforms = platforms.all;
-    mainProgram = "gremlin-console";
-  };
-}

pkgs/applications/misc/gremlin-server/default.nix

···
-{
-  fetchzip,
-  lib,
-  stdenv,
-  makeWrapper,
-  openjdk,
-}:
-stdenv.mkDerivation rec {
-  pname = "gremlin-server";
-  version = "3.7.0";
-  src = fetchzip {
-    url = "https://downloads.apache.org/tinkerpop/${version}/apache-tinkerpop-gremlin-server-${version}-bin.zip";
-    sha256 = "sha256-cS7R7Raz5tkrr5DNeW7jbEYDee2OgE4htTXJRnqXlqI=";
-  };
-
-  nativeBuildInputs = [ makeWrapper ];
-
-  # Note you'll want to prefix any commands with LOG_DIR, PID_DIR, and RUN_DIR
-  # environment variables set to a writable director(y/ies).
-
-  installPhase = ''
-    runHook preInstall
-    mkdir -p $out/opt
-    cp -r conf ext lib scripts $out/opt/
-    install -D bin/gremlin-server.sh $out/opt/bin/gremlin-server
-    makeWrapper $out/opt/bin/gremlin-server $out/bin/gremlin-server \
-      --prefix PATH ":" "${openjdk}/bin/" \
-      --set CLASSPATH "$out/opt/lib/"
-    runHook postInstall
-  '';
-
-  meta = with lib; {
-    homepage = "https://tinkerpop.apache.org/";
-    description = "Server of the Apache TinkerPop graph computing framework";
-    license = licenses.asl20;
-    maintainers = [ maintainers.jrpotter ];
-    platforms = platforms.all;
-    mainProgram = "gremlin-server";
-  };
-}

pkgs/applications/misc/keystore-explorer/default.nix

···
-{
-  fetchzip,
-  lib,
-  stdenv,
-  jdk,
-  runtimeShell,
-  glib,
-  wrapGAppsHook3,
-}:
-
-stdenv.mkDerivation rec {
-  version = "5.6.0";
-  pname = "keystore-explorer";
-  src = fetchzip {
-    url = "https://github.com/kaikramer/keystore-explorer/releases/download/v${version}/kse-${
-      lib.replaceStrings [ "." ] [ "" ] version
-    }.zip";
-    sha256 = "sha256-+ZgALJaZodLmAtdCIE1SG6D0lzlETg4mMPXheXmGhPc=";
-  };
-
-  # glib is necessary so file dialogs don't hang.
-  buildInputs = [ glib ];
-  nativeBuildInputs = [ wrapGAppsHook3 ];
-
-  installPhase = ''
-    runHook preInstall
-
-    mkdir -p $out/bin
-    mkdir -p $out/share/keystore-explorer
-    cp -R icons licenses lib kse.jar $out/share/keystore-explorer/
-
-    # keystore-explorer's kse.sh tries to detect the path of Java by using
-    # Python on Darwin; just write our own start script to avoid unnecessary dependencies
-    cat > $out/bin/keystore-explorer <<EOF
-    #!${runtimeShell}
-    export JAVA_HOME=${jdk.home}
-    exec ${jdk}/bin/java -jar $out/share/keystore-explorer/kse.jar "\$@"
-    EOF
-    chmod +x $out/bin/keystore-explorer
-
-    runHook postInstall
-  '';
-
-  dontStrip = true;
-  dontBuild = true;
-  dontConfigure = true;
-
-  meta = {
-    description = "Open source GUI replacement for the Java command-line utilities keytool and jarsigner";
-    mainProgram = "keystore-explorer";
-    sourceProvenance = with lib.sourceTypes; [ binaryBytecode ];
-    license = lib.licenses.gpl3Only;
-    maintainers = [ lib.maintainers.numinit ];
-    platforms = lib.platforms.unix;
-  };
-}

pkgs/applications/misc/pattypan/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  ant,
-  jdk,
-  makeWrapper,
-  wrapGAppsHook3,
-  makeDesktopItem,
-  copyDesktopItems,
-  stripJavaArchivesHook,
-}:
-
-stdenv.mkDerivation (finalAttrs: {
-  pname = "pattypan";
-  version = "22.03";
-
-  src = fetchFromGitHub {
-    owner = "yarl";
-    repo = "pattypan";
-    rev = "v${finalAttrs.version}";
-    hash = "sha256-wMQrBg+rEV1W7NgtWFXZr3pAxpyqdbEBKLNwDDGju2I=";
-  };
-
-  nativeBuildInputs = [
-    ant
-    jdk
-    makeWrapper
-    wrapGAppsHook3
-    copyDesktopItems
-    stripJavaArchivesHook
-  ];
-
-  dontWrapGApps = true;
-
-  env.JAVA_TOOL_OPTIONS = "-Dfile.encoding=UTF8"; # needed for jdk versions below jdk19
-
-  buildPhase = ''
-    runHook preBuild
-    ant
-    runHook postBuild
-  '';
-
-  installPhase = ''
-    runHook preInstall
-    install -Dm644 pattypan.jar -t $out/share/pattypan
-    install -Dm644 src/pattypan/resources/logo.png $out/share/pixmaps/pattypan.png
-    runHook postInstall
-  '';
-
-  # gappsWrapperArgs is set in preFixup
-  postFixup = ''
-    makeWrapper ${jdk}/bin/java $out/bin/pattypan \
-        ''${gappsWrapperArgs[@]} \
-        --add-flags "-jar $out/share/pattypan/pattypan.jar"
-  '';
-
-  desktopItems = [
-    (makeDesktopItem {
-      name = "pattypan";
-      exec = "pattypan";
-      icon = "pattypan";
-      desktopName = "Pattypan";
-      genericName = "An uploader for Wikimedia Commons";
-      categories = [ "Utility" ];
-    })
-  ];
-
-  meta = with lib; {
-    description = "Uploader for Wikimedia Commons";
-    homepage = "https://commons.wikimedia.org/wiki/Commons:Pattypan";
-    license = licenses.mit;
-    mainProgram = "pattypan";
-    maintainers = with maintainers; [ fee1-dead ];
-    platforms = platforms.all;
-    sourceProvenance = with sourceTypes; [
-      fromSource
-      binaryBytecode # source bundles dependencies as jars
-    ];
-  };
-})

pkgs/applications/networking/davmail/default.nix

···
-{
-  stdenv,
-  fetchzip,
-  lib,
-  makeWrapper,
-  unzip,
-  glib,
-  gtk2,
-  gtk3,
-  jre,
-  libXtst,
-  coreutils,
-  gnugrep,
-  zulu,
-  preferGtk3 ? true,
-  preferZulu ? true,
-}:
-
-let
-  rev = 3627;
-  jre' = if preferZulu then zulu else jre;
-  gtk' = if preferGtk3 then gtk3 else gtk2;
-in
-stdenv.mkDerivation rec {
-  pname = "davmail";
-  version = "6.3.0";
-
-  src = fetchzip {
-    url = "mirror://sourceforge/${pname}/${version}/${pname}-${version}-${toString rev}.zip";
-    hash = "sha256-zJMwCFX/uJnLeThj6/t2usBRM+LIuamZt0EFLG3N+8k=";
-    stripRoot = false;
-  };
-
-  postPatch = ''
-    sed -i -e '/^JAVA_OPTS/d' davmail
-  '';
-
-  nativeBuildInputs = [
-    makeWrapper
-    unzip
-  ];
-
-  installPhase = ''
-    runHook preInstall
-
-    mkdir -p $out/share/davmail
-    cp -vR ./* $out/share/davmail
-    makeWrapper $out/share/davmail/davmail $out/bin/davmail \
-      --set-default JAVA_OPTS "-Xmx512M -Dsun.net.inetaddr.ttl=60 -Djdk.gtk.version=${lib.versions.major gtk'.version}" \
-      --prefix PATH : ${
-        lib.makeBinPath [
-          jre'
-          coreutils
-          gnugrep
-        ]
-      } \
-      --prefix LD_LIBRARY_PATH : ${
-        lib.makeLibraryPath [
-          glib
-          gtk'
-          libXtst
-        ]
-      }
-
-    runHook postInstall
-  '';
-
-  meta = with lib; {
-    description = "Java application which presents a Microsoft Exchange server as local CALDAV, IMAP and SMTP servers";
-    homepage = "https://davmail.sourceforge.net/";
-    license = licenses.gpl2Plus;
-    maintainers = with maintainers; [ peterhoeg ];
-    platforms = platforms.all;
-    mainProgram = "davmail";
-  };
-}

pkgs/applications/office/jabref/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  wrapGAppsHook3,
-  makeDesktopItem,
-  copyDesktopItems,
-  unzip,
-  xdg-utils,
-  gtk3,
-  jdk,
-  gradle_8,
-  python3,
-}:
-let
-  # "Deprecated Gradle features were used in this build, making it incompatible with Gradle 9.0."
-  gradle = gradle_8;
-in
-stdenv.mkDerivation rec {
-  version = "5.13";
-  pname = "jabref";
-
-  src = fetchFromGitHub {
-    owner = "JabRef";
-    repo = "jabref";
-    rev = "v${version}";
-    hash = "sha256-inE2FXAaEEiq7343KwtjEiTEHLtn01AzP0foTpsLoAw=";
-    fetchSubmodules = true;
-  };
-
-  desktopItems = [
-    (makeDesktopItem {
-      comment = meta.description;
-      name = "JabRef";
-      desktopName = "JabRef";
-      genericName = "Bibliography manager";
-      categories = [ "Office" ];
-      icon = "jabref";
-      exec = "JabRef %U";
-      startupWMClass = "org.jabref.gui.JabRefGUI";
-      mimeTypes = [ "text/x-bibtex" ];
-    })
-  ];
-
-  mitmCache = gradle.fetchDeps {
-    inherit pname;
-    data = ./deps.json;
-  };
-
-  postPatch = ''
-    # Disable update check
-    substituteInPlace src/main/java/org/jabref/preferences/JabRefPreferences.java \
-      --replace 'VERSION_CHECK_ENABLED, Boolean.TRUE' \
-        'VERSION_CHECK_ENABLED, Boolean.FALSE'
-
-    # Find OpenOffice/LibreOffice binary
-    substituteInPlace src/main/java/org/jabref/logic/openoffice/OpenOfficePreferences.java \
-      --replace '/usr' '/run/current-system/sw'
-  '';
-
-  nativeBuildInputs = [
-    jdk
-    gradle
-    wrapGAppsHook3
-    copyDesktopItems
-    unzip
-  ];
-
-  buildInputs = [
-    gtk3
-    python3
-  ];
-
-  gradleFlags = [
-    "-PprojVersion=${version}"
-    "-Dorg.gradle.java.home=${jdk}"
-  ];
-
-  preBuild = ''
-    gradleFlagsArray+=(-PprojVersionInfo="${version} NixOS")
-  '';
-
-  dontWrapGApps = true;
-
-  installPhase = ''
-    runHook preInstall
-
-    install -dm755 $out/share/java/jabref
-    install -Dm644 LICENSE $out/share/licenses/jabref/LICENSE
-    install -Dm644 src/main/resources/icons/jabref.svg $out/share/pixmaps/jabref.svg
-
-    # script to support browser extensions
-    install -Dm755 buildres/linux/jabrefHost.py $out/lib/jabrefHost.py
-    patchShebangs $out/lib/jabrefHost.py
-    install -Dm644 buildres/linux/native-messaging-host/firefox/org.jabref.jabref.json $out/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json
-    sed -i -e "s|/opt/jabref|$out|" $out/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json
-
-    # Resources in the jar can't be found, workaround copied from AUR
-    cp -r build/resources $out/share/java/jabref
-
-    tar xf build/distributions/JabRef-${version}.tar -C $out --strip-components=1
-
-    DEFAULT_JVM_OPTS=$(sed -n -E "s/^DEFAULT_JVM_OPTS='(.*)'$/\1/p" $out/bin/JabRef | sed -e "s|\$APP_HOME|$out|g" -e 's/"//g')
-
-    # Temp fix: openjfx doesn't build with webkit
-    unzip $out/lib/javafx-web-*-*.jar libjfxwebkit.so -d $out/lib/
-
-    runHook postInstall
-  '';
-
-  postFixup = ''
-    rm $out/bin/*
-
-    # put this in postFixup because some gappsWrapperArgs are generated in gappsWrapperArgsHook in preFixup
-    makeWrapper ${jdk}/bin/java $out/bin/JabRef \
-      "''${gappsWrapperArgs[@]}" \
-      --suffix PATH : ${lib.makeBinPath [ xdg-utils ]} \
-      --add-flags "-Djava.library.path=$out/lib/ --patch-module org.jabref=$out/share/java/jabref/resources/main" \
-      --add-flags "$DEFAULT_JVM_OPTS"
-
-    # lowercase alias (for convenience and required for browser extensions)
-    ln -sf $out/bin/JabRef $out/bin/jabref
-  '';
-
-  gradleUpdateScript = ''
-    runHook preBuild
-
-    gradle nixDownloadDeps -Dos.arch=amd64
-    gradle nixDownloadDeps -Dos.arch=aarch64
-  '';
-
-  meta = with lib; {
-    description = "Open source bibliography reference manager";
-    homepage = "https://www.jabref.org";
-    sourceProvenance = with sourceTypes; [
-      fromSource
-      binaryBytecode # source bundles dependencies as jars
-      binaryNativeCode # source bundles dependencies as jars
-    ];
-    license = licenses.mit;
-    platforms = [
-      "x86_64-linux"
-      "aarch64-linux"
-    ];
-    maintainers = with maintainers; [
-      linsui
-    ];
-  };
-}

pkgs/applications/science/biology/trimmomatic/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  ant,
-  jdk,
-  jre,
-  makeWrapper,
-  stripJavaArchivesHook,
-}:
-
-stdenv.mkDerivation (finalAttrs: {
-  pname = "trimmomatic";
-  version = "0.39";
-
-  src = fetchFromGitHub {
-    owner = "usadellab";
-    repo = "Trimmomatic";
-    rev = "v${finalAttrs.version}";
-    hash = "sha256-u+ubmacwPy/vsEi0YQCv0fTnVDesQvqeQDEwCbS8M6I=";
-  };
-
-  # Remove jdk version requirement
-  postPatch = ''
-    substituteInPlace ./build.xml \
-      --replace 'source="1.5" target="1.5"' ""
-  '';
-
-  nativeBuildInputs = [
-    ant
-    jdk
-    makeWrapper
-    stripJavaArchivesHook
-  ];
-
-  buildPhase = ''
-    runHook preBuild
-
-    ant
-
-    runHook postBuild
-  '';
-
-  installPhase = ''
-    runHook preInstall
-
-    install -Dm644 dist/jar/trimmomatic-*.jar -t $out/share/trimmomatic
-    cp -r adapters $out/share/trimmomatic
-
-    makeWrapper ${jre}/bin/java $out/bin/trimmomatic \
-        --add-flags "-jar $out/share/trimmomatic/trimmomatic-*.jar"
-
-    runHook postInstall
-  '';
-
-  meta = {
-    changelog = "https://github.com/usadellab/Trimmomatic/blob/main/versionHistory.txt";
-    description = "Flexible read trimming tool for Illumina NGS data";
-    longDescription = ''
-      Trimmomatic performs a variety of useful trimming tasks for illumina
-      paired-end and single ended data: adapter trimming, quality trimming,
-      cropping to a specified length, length filtering, quality score
-      conversion.
-    '';
-    homepage = "http://www.usadellab.org/cms/?page=trimmomatic";
-    downloadPage = "https://github.com/usadellab/Trimmomatic/releases";
-    license = lib.licenses.gpl3Only;
-    sourceProvenance = [
-      lib.sourceTypes.fromSource
-      lib.sourceTypes.binaryBytecode # source bundles dependencies as jars
-    ];
-    mainProgram = "trimmomatic";
-    maintainers = [ lib.maintainers.kupac ];
-  };
-})

pkgs/applications/science/misc/openrefine/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  buildNpmPackage,
-  curl,
-  jdk,
-  jq,
-  makeWrapper,
-  maven,
-}:
-
-let
-  version = "3.9.5";
-  src = fetchFromGitHub {
-    owner = "openrefine";
-    repo = "openrefine";
-    rev = version;
-    hash = "sha256-548vOJf0mlk1AuuMjEXpsiVjft6UbJrUxh5mSca8Xbw=";
-  };
-
-  npmPkg = buildNpmPackage {
-    inherit src version;
-
-    pname = "openrefine-npm";
-    sourceRoot = "${src.name}/main/webapp";
-
-    npmDepsHash = "sha256-I0iqGniXeqyCWf1DG2nMNkTScCrtJYeYF9n2Zt6Syjc=";
-
-    # package.json doesn't supply a version, which npm doesn't like - fix this.
-    # directly referencing jq because buildNpmPackage doesn't pass
-    # nativeBuildInputs through to fetchNpmDeps
-    postPatch = ''
-      NEW_PACKAGE_JSON=$(mktemp)
-      ${jq}/bin/jq '. + {version: $ENV.version}' package.json > $NEW_PACKAGE_JSON
-      cp $NEW_PACKAGE_JSON package.json
-    '';
-
-    dontNpmBuild = true;
-    installPhase = ''
-      mkdir -p $out
-      cp -r modules/core/3rdparty/* $out/
-    '';
-  };
-
-in
-maven.buildMavenPackage {
-  inherit src version;
-
-  pname = "openrefine";
-
-  postPatch = ''
-    cp -r ${npmPkg} main/webapp/modules/core/3rdparty
-  '';
-
-  mvnJdk = jdk;
-  mvnParameters = "-pl !packaging";
-  mvnHash = "sha256-SV5nfyUeyRul/YfZZXor8O37ARdCtKkrHCLzQrmr96s=";
-
-  nativeBuildInputs = [ makeWrapper ];
-
-  doCheck = false;
-
-  installPhase = ''
-    mkdir -p $out/lib/server/target/lib
-    cp -r server/target/lib/* $out/lib/server/target/lib/
-    cp server/target/openrefine-*-server.jar $out/lib/server/target/lib/
-
-    mkdir -p $out/lib/webapp
-    cp -r main/webapp/{WEB-INF,modules} $out/lib/webapp/
-    (
-      cd extensions
-      for ext in * ; do
-        if [ -d "$ext/module" ] ; then
-          mkdir -p "$out/lib/webapp/extensions/$ext"
-          cp -r "$ext/module" "$out/lib/webapp/extensions/$ext/"
-        fi
-      done
-    )
-
-    mkdir -p $out/etc
-    cp refine.ini $out/etc/
-
-    mkdir -p $out/bin
-    cp refine $out/bin/
-  '';
-
-  preFixup = ''
-    find $out -name '*.java' -delete
-    sed -i -E 's|^(butterfly\.modules\.path =).*extensions.*$|\1 '"$out/lib/webapp/extensions|" \
-      $out/lib/webapp/WEB-INF/butterfly.properties
-
-    sed -i 's|^cd `dirname \$0`$|cd '"$out/lib|" $out/bin/refine
-
-    cat >> $out/etc/refine.ini <<EOF
-    REFINE_WEBAPP='$out/lib/webapp'
-    REFINE_LIB_DIR='$out/lib/server/target/lib'
-
-    JAVA_HOME='${jdk.home}'
-
-    # non-headless mode tries to launch a browser, causing a
-    # number of purity problems
-    JAVA_OPTIONS='-Drefine.headless=true'
-    EOF
-
-    wrapProgram $out/bin/refine \
-      --prefix PATH : '${
-        lib.makeBinPath [
-          jdk
-          curl
-        ]
-      }' \
-      --set-default REFINE_INI_PATH "$out/etc/refine.ini"
-  '';
-
-  passthru = {
-    inherit npmPkg;
-    updateScript = ./update.sh;
-  };
-
-  meta = with lib; {
-    description = "Power tool for working with messy data and improving it";
-    homepage = "https://openrefine.org";
-    license = licenses.bsd3;
-    maintainers = with maintainers; [
-      ris
-      arcstur
-    ];
-    sourceProvenance = with sourceTypes; [
-      fromSource
-      binaryBytecode # maven dependencies
-    ];
-    broken = stdenv.hostPlatform.isDarwin; # builds, doesn't run
-    mainProgram = "refine";
-  };
-}

pkgs/by-name/ad/adoptopenjdk-icedtea-web/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cargo,
+  rustc,
+  autoreconfHook,
+  jdk8,
+  glib,
+  firefox-unwrapped,
+  zip,
+  pkg-config,
+  npapi_sdk,
+  bash,
+  bc,
+}:
+let
+  jdk = jdk8;
+in
+stdenv.mkDerivation rec {
+  pname = "adoptopenjdk-icedtea-web";
+
+  version = "1.8.8";
+
+  src = fetchFromGitHub {
+    owner = "AdoptOpenJDK";
+    repo = "IcedTea-Web";
+    rev = "icedtea-web-${version}";
+    sha256 = "sha256-hpEVWG9ltNDL/0EFJjgQRRce+BLcCO4ZERULYZxyC1o=";
+  };
+
+  nativeBuildInputs = [
+    autoreconfHook
+    pkg-config
+    bc
+  ];
+  buildInputs = [
+    cargo
+    rustc
+    glib
+    firefox-unwrapped
+    zip
+    npapi_sdk
+  ];
+
+  preConfigure = ''
+    configureFlagsArray+=("BIN_BASH=${bash}/bin/bash")
+  '';
+
+  patches = [ ./patches/0001-make-cargo-work-with-nix-build-on-linux.patch ];
+
+  doCheck = true;
+  preCheck = ''
+    # Needed for the below rust-launcher tests to pass
+    # dirs_paths_helper::tests::check_config_files_paths
+    # dirs_paths_helper::tests::check_legacy_config_files_paths
+
+    mkdir -p $HOME/.icedtea
+    touch $HOME/.icedtea/deployment.properties
+
+    mkdir -p $XDG_CONFIG_HOME/icedtea-web
+    touch $XDG_CONFIG_HOME/icedtea-web/deployment.properties
+  '';
+
+  HOME = "/build";
+  XDG_CONFIG_HOME = "/build";
+
+  configureFlags = [
+    "--with-itw-libs=DISTRIBUTION"
+    "--with-jdk-home=${jdk.home}"
+    "--disable-docs"
+  ];
+
+  mozillaPlugin = "/lib";
+
+  postInstall = ''
+    mkdir -p $out/share/applications
+    cp javaws.desktop itweb-settings.desktop policyeditor.desktop $out/share/applications
+  '';
+
+  meta = {
+    description = "Java web browser plugin and an implementation of Java Web Start";
+    longDescription = ''
+      A Free Software web browser plugin running applets written in the Java
+      programming language and an implementation of Java Web Start, originally
+      based on the NetX project.
+    '';
+    homepage = "https://github.com/adoptopenjdk/icedtea-web";
+    platforms = lib.platforms.linux;
+  };
+}

pkgs/by-name/ba/ballerina/package.nix

···
+{
+  ballerina,
+  lib,
+  writeText,
+  runCommand,
+  makeWrapper,
+  fetchzip,
+  stdenv,
+  openjdk17_headless,
+}:
+let
+  version = "2201.10.3";
+  codeName = "swan-lake";
+  openjdk = openjdk17_headless;
+in
+stdenv.mkDerivation {
+  pname = "ballerina";
+  inherit version;
+
+  src = fetchzip {
+    url = "https://dist.ballerina.io/downloads/${version}/ballerina-${version}-${codeName}.zip";
+    hash = "sha256-JVwxWRiOQaUZBkvxoLhKvktyQYnBtbCBZXZa6g6hoRQ=";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  installPhase = ''
+    runHook preInstall
+    cp -rv distributions/ballerina-${version} $out
+    runHook postInstall
+  '';
+  preFixup = ''
+    wrapProgram $out/bin/bal --set JAVA_HOME ${openjdk}
+  '';
+
+  passthru.tests.smokeTest =
+    let
+      helloWorld = writeText "hello-world.bal" ''
+        import ballerina/io;
+        public function main() {
+          io:println("Hello, World!");
+        }
+      '';
+    in
+    runCommand "ballerina-${version}-smoketest" { } ''
+      ${ballerina}/bin/bal run ${helloWorld} >$out
+      read result <$out
+      [[ $result = "Hello, World!" ]]
+    '';
+
+  meta = with lib; {
+    description = "Open-source programming language for the cloud";
+    mainProgram = "bal";
+    license = licenses.asl20;
+    platforms = openjdk.meta.platforms;
+    maintainers = with maintainers; [ eigengrau ];
+    sourceProvenance = with sourceTypes; [ binaryBytecode ];
+  };
+}

pkgs/by-name/da/davmail/package.nix

···
+{
+  stdenv,
+  fetchzip,
+  lib,
+  makeWrapper,
+  unzip,
+  glib,
+  gtk2,
+  gtk3,
+  jdk11,
+  libXtst,
+  coreutils,
+  gnugrep,
+  zulu11,
+  preferGtk3 ? true,
+  preferZulu ? true,
+}:
+
+let
+  rev = 3627;
+  jre' = (if preferZulu then zulu11 else jdk11).override { enableJavaFX = true; };
+  gtk' = if preferGtk3 then gtk3 else gtk2;
+in
+stdenv.mkDerivation rec {
+  pname = "davmail";
+  version = "6.3.0";
+
+  src = fetchzip {
+    url = "mirror://sourceforge/${pname}/${version}/${pname}-${version}-${toString rev}.zip";
+    hash = "sha256-zJMwCFX/uJnLeThj6/t2usBRM+LIuamZt0EFLG3N+8k=";
+    stripRoot = false;
+  };
+
+  postPatch = ''
+    sed -i -e '/^JAVA_OPTS/d' davmail
+  '';
+
+  nativeBuildInputs = [
+    makeWrapper
+    unzip
+  ];
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/share/davmail
+    cp -vR ./* $out/share/davmail
+    makeWrapper $out/share/davmail/davmail $out/bin/davmail \
+      --set-default JAVA_OPTS "-Xmx512M -Dsun.net.inetaddr.ttl=60 -Djdk.gtk.version=${lib.versions.major gtk'.version}" \
+      --prefix PATH : ${
+        lib.makeBinPath [
+          jre'
+          coreutils
+          gnugrep
+        ]
+      } \
+      --prefix LD_LIBRARY_PATH : ${
+        lib.makeLibraryPath [
+          glib
+          gtk'
+          libXtst
+        ]
+      }
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Java application which presents a Microsoft Exchange server as local CALDAV, IMAP and SMTP servers";
+    homepage = "https://davmail.sourceforge.net/";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ peterhoeg ];
+    platforms = platforms.all;
+    mainProgram = "davmail";
+  };
+}

pkgs/by-name/di/DisnixWebService/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch,
+  ant,
+  jdk8,
+  xmlstarlet,
+  axis2,
+  dbus_java,
+}:
+let
+  jdk = jdk8;
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "DisnixWebService";
+  version = "0.10.1";
+
+  src = fetchFromGitHub {
+    owner = "svanderburg";
+    repo = "DisnixWebService";
+    rev = "DisnixWebService-${finalAttrs.version}";
+    hash = "sha256-zcYr2Ytx4pevSthTQLpnQ330wDxN9dWsZA20jbO6PxQ=";
+  };
+
+  patches = [
+    # Correct the DisnixWebService build for compatibility with Axis2 1.8.1
+    # See https://github.com/svanderburg/DisnixWebService/pull/2
+    (fetchpatch {
+      url = "https://github.com/svanderburg/DisnixWebService/commit/cee99c6af744b5dda16728a70ebd2800f61871a0.patch";
+      hash = "sha256-4rSEN8AwivUXUCIUYFBRIoE19jVDv+Vpgakmy8fR06A=";
+    })
+  ];
+
+  nativeBuildInputs = [
+    ant
+    jdk
+    xmlstarlet
+  ];
+
+  env = {
+    PREFIX = "\${env.out}";
+    AXIS2_LIB = "${axis2}/lib";
+    AXIS2_WEBAPP = "${axis2}/webapps/axis2";
+    DBUS_JAVA_LIB = "${dbus_java}/share/java";
+  };
+
+  prePatch = ''
+    # add modificationtime="0" to the <jar> and <war> tasks to achieve reproducibility
+    xmlstarlet ed -L -a "//jar|//war" -t attr -n "modificationtime" -v "0" build.xml
+
+    sed -i -e "s|#JAVA_HOME=|JAVA_HOME=${jdk}|" \
+       -e "s|#AXIS2_LIB=|AXIS2_LIB=${axis2}/lib|" \
+        scripts/disnix-soap-client
+  '';
+
+  buildPhase = ''
+    runHook preBuild
+    ant
+    runHook postBuild
+  '';
+
+  installPhase = ''
+    runHook preInstall
+    ant install
+    runHook postInstall
+  '';
+
+  meta = {
+    description = "SOAP interface and client for Disnix";
+    mainProgram = "disnix-soap-client";
+    homepage = "https://github.com/svanderburg/DisnixWebService";
+    changelog = "https://github.com/svanderburg/DisnixWebService/blob/${finalAttrs.src.rev}/NEWS.txt";
+    license = lib.licenses.mit;
+    maintainers = [ lib.maintainers.sander ];
+    platforms = lib.platforms.linux;
+  };
+})

pkgs/by-name/el/elasticmq-server-bin/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchurl,
+  jdk8,
+  jre8,
+  makeBinaryWrapper,
+  runCommand,
+  python3Packages,
+  writeText,
+}:
+let
+  jre = jre8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+  jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "elasticmq-server";
+  version = "1.6.14";
+
+  src = fetchurl {
+    url = "https://s3-eu-west-1.amazonaws.com/softwaremill-public/elasticmq-server-${finalAttrs.version}.jar";
+    sha256 = "sha256-HVllLHz6zutonaLFwgyQKYSZxfp5QMslxf/PlzGWyG4=";
+  };
+
+  # don't do anything?
+  unpackPhase = "${jdk}/bin/jar xf $src favicon.png";
+
+  nativeBuildInputs = [ makeBinaryWrapper ];
+
+  installPhase = ''
+    mkdir -p $out/bin $out/share/elasticmq-server
+
+    cp $src $out/share/elasticmq-server/elasticmq-server.jar
+
+    # TODO: how to add extraArgs? current workaround is to use JAVA_TOOL_OPTIONS environment to specify properties
+    makeWrapper ${jre}/bin/java $out/bin/elasticmq-server \
+      --add-flags "-jar $out/share/elasticmq-server/elasticmq-server.jar"
+  '';
+
+  passthru.tests.elasticmqTest = import ./elasticmq-test.nix {
+    inherit runCommand python3Packages writeText;
+    elasticmq-server = finalAttrs.finalPackage;
+  };
+
+  meta = with lib; {
+    description = "Message queueing system with Java, Scala and Amazon SQS-compatible interfaces";
+    homepage = "https://github.com/softwaremill/elasticmq";
+    changelog = "https://github.com/softwaremill/elasticmq/releases/tag/v${finalAttrs.version}";
+    sourceProvenance = with sourceTypes; [ binaryBytecode ];
+    license = licenses.asl20;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ peterromfeldhk ];
+    mainProgram = "elasticmq-server";
+  };
+})

pkgs/by-name/en/envoy/package.nix

···
   cmake,
   gn,
   go,
-  jdk,
+  openjdk11_headless,
   ninja,
   patchelf,
   python312,
···
       .${stdenv.system} or (throw "unsupported system ${stdenv.system}");
 
   python3 = python312;
+  jdk = openjdk11_headless;
 
 in
 buildBazelPackage rec {

pkgs/by-name/ga/ganttproject-bin/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchzip,
+  makeDesktopItem,
+  makeWrapper,
+  openjdk17,
+}:
+let
+  jre = openjdk17.override {
+    enableJavaFX = true;
+  };
+in
+stdenv.mkDerivation rec {
+  pname = "ganttproject-bin";
+  version = "3.3.3316";
+
+  src = fetchzip {
+    url = "https://dl.ganttproject.biz/ganttproject-${version}/ganttproject-${version}.zip";
+    stripRoot = false;
+    hash = "sha256-tiEq/xdC0gXiUInLS9xGR/vI/BpdSA+mSf5yukuejc4=";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre ];
+
+  installPhase =
+    let
+
+      desktopItem = makeDesktopItem {
+        name = "ganttproject";
+        exec = "ganttproject";
+        icon = "ganttproject";
+        desktopName = "GanttProject";
+        genericName = "Shedule and manage projects";
+        comment = meta.description;
+        categories = [ "Office" ];
+      };
+
+      javaOptions = [
+        "-Dawt.useSystemAAFontSettings=gasp"
+      ];
+
+    in
+    ''
+      mkdir -pv "$out/share/ganttproject"
+      cp -rv *  "$out/share/ganttproject"
+
+      mkdir -pv "$out/bin"
+      wrapProgram "$out/share/ganttproject/ganttproject" \
+        --set JAVA_HOME "${jre}" \
+        --prefix _JAVA_OPTIONS " " "${builtins.toString javaOptions}"
+
+      mv -v "$out/share/ganttproject/ganttproject" "$out/bin"
+
+      cp -rv "${desktopItem}/share/applications" "$out/share"
+    '';
+
+  meta = with lib; {
+    description = "Project scheduling and management";
+    homepage = "https://www.ganttproject.biz/";
+    downloadPage = "https://www.ganttproject.biz/download";
+    # GanttProject itself is GPL3+. All bundled libraries are declared
+    # ‘GPL3-compatible’. See ${downloadPage} for detailed information.
+    license = licenses.gpl3Plus;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.vidbina ];
+    mainProgram = "ganttproject";
+  };
+}

pkgs/by-name/gr/greenfoot/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchurl,
+  openjdk21,
+  openjfx21,
+  glib,
+  dpkg,
+  wrapGAppsHook3,
+}:
+let
+  openjdk = openjdk21.override {
+    enableJavaFX = true;
+    openjfx_jdk = openjfx21.override { withWebKit = true; };
+  };
+in
+stdenv.mkDerivation rec {
+  pname = "greenfoot";
+  version = "3.9.0";
+
+  src = fetchurl {
+    # We use the deb here. First instinct might be to go for the "generic" JAR
+    # download, but that is actually a graphical installer that is much harder
+    # to unpack than the deb.
+    url = "https://www.greenfoot.org/download/files/Greenfoot-linux-arm64-${
+      builtins.replaceStrings [ "." ] [ "" ] version
+    }.deb";
+    hash = "sha256-d5bkK+teTA4fxFb46ovbZE28l8WILGStv3Vg3nJZfv0=";
+  };
+
+  nativeBuildInputs = [
+    dpkg
+    wrapGAppsHook3
+  ];
+  buildInputs = [ glib ];
+
+  dontWrapGApps = true;
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out
+    cp -r usr/* $out
+
+    rm -r $out/share/greenfoot/jdk
+    rm -r $out/share/greenfoot/javafx-*.jar
+
+    makeWrapper ${openjdk}/bin/java $out/bin/greenfoot \
+      "''${gappsWrapperArgs[@]}" \
+      --add-flags "-Dawt.useSystemAAFontSettings=gasp -Xmx512M \
+                   --add-opens javafx.graphics/com.sun.glass.ui=ALL-UNNAMED \
+                   -cp $out/share/greenfoot/boot.jar bluej.Boot \
+                   -greenfoot=true -bluej.compiler.showunchecked=false \
+                   -greenfoot.scenarios=$out/share/doc/Greenfoot/scenarios \
+                   -greenfoot.url.javadoc=file://$out/share/doc/Greenfoot/API"
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Simple integrated development environment for Java";
+    homepage = "https://www.greenfoot.org/";
+    sourceProvenance = with sourceTypes; [ binaryBytecode ];
+    license = with licenses; [
+      gpl2Plus
+      classpathException20
+    ];
+    mainProgram = "greenfoot";
+    maintainers = [ maintainers.chvp ];
+    platforms = platforms.linux;
+  };
+}

pkgs/by-name/gr/gremlin-console/package.nix

···
+{
+  fetchzip,
+  lib,
+  stdenv,
+  makeWrapper,
+  openjdk11,
+}:
+let
+  openjdk = openjdk11;
+in
+stdenv.mkDerivation rec {
+  pname = "gremlin-console";
+  version = "3.7.4";
+  src = fetchzip {
+    url = "https://downloads.apache.org/tinkerpop/${version}/apache-tinkerpop-gremlin-console-${version}-bin.zip";
+    sha256 = "sha256-Z971M4W359WKs2NjLeWej5IVHnFu5LLsffxl0jraB60=";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $out/opt
+    cp -r ext lib $out/opt/
+    install -D bin/gremlin.sh $out/opt/bin/gremlin-console
+    makeWrapper $out/opt/bin/gremlin-console $out/bin/gremlin-console \
+      --prefix PATH ":" "${openjdk}/bin/" \
+      --set CLASSPATH "$out/opt/lib/"
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    homepage = "https://tinkerpop.apache.org/";
+    description = "Console of the Apache TinkerPop graph computing framework";
+    license = licenses.asl20;
+    maintainers = [ maintainers.lewo ];
+    platforms = platforms.all;
+    mainProgram = "gremlin-console";
+  };
+}

pkgs/by-name/gr/gremlin-server/package.nix

···
+{
+  fetchzip,
+  lib,
+  stdenv,
+  makeWrapper,
+  openjdk11,
+}:
+let
+  openjdk = openjdk11;
+in
+stdenv.mkDerivation rec {
+  pname = "gremlin-server";
+  version = "3.7.0";
+  src = fetchzip {
+    url = "https://downloads.apache.org/tinkerpop/${version}/apache-tinkerpop-gremlin-server-${version}-bin.zip";
+    sha256 = "sha256-cS7R7Raz5tkrr5DNeW7jbEYDee2OgE4htTXJRnqXlqI=";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  # Note you'll want to prefix any commands with LOG_DIR, PID_DIR, and RUN_DIR
+  # environment variables set to a writable director(y/ies).
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $out/opt
+    cp -r conf ext lib scripts $out/opt/
+    install -D bin/gremlin-server.sh $out/opt/bin/gremlin-server
+    makeWrapper $out/opt/bin/gremlin-server $out/bin/gremlin-server \
+      --prefix PATH ":" "${openjdk}/bin/" \
+      --set CLASSPATH "$out/opt/lib/"
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    homepage = "https://tinkerpop.apache.org/";
+    description = "Server of the Apache TinkerPop graph computing framework";
+    license = licenses.asl20;
+    maintainers = [ maintainers.jrpotter ];
+    platforms = platforms.all;
+    mainProgram = "gremlin-server";
+  };
+}

pkgs/by-name/ja/jabref/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  wrapGAppsHook3,
+  makeDesktopItem,
+  copyDesktopItems,
+  unzip,
+  xdg-utils,
+  gtk3,
+  jdk21,
+  openjfx23,
+  gradle_8,
+  python3,
+}:
+let
+  jdk = jdk21.override {
+    enableJavaFX = true;
+    openjfx_jdk = openjfx23;
+  };
+  # "Deprecated Gradle features were used in this build, making it incompatible with Gradle 9.0."
+  gradle = gradle_8;
+in
+stdenv.mkDerivation rec {
+  version = "5.13";
+  pname = "jabref";
+
+  src = fetchFromGitHub {
+    owner = "JabRef";
+    repo = "jabref";
+    rev = "v${version}";
+    hash = "sha256-inE2FXAaEEiq7343KwtjEiTEHLtn01AzP0foTpsLoAw=";
+    fetchSubmodules = true;
+  };
+
+  desktopItems = [
+    (makeDesktopItem {
+      comment = meta.description;
+      name = "JabRef";
+      desktopName = "JabRef";
+      genericName = "Bibliography manager";
+      categories = [ "Office" ];
+      icon = "jabref";
+      exec = "JabRef %U";
+      startupWMClass = "org.jabref.gui.JabRefGUI";
+      mimeTypes = [ "text/x-bibtex" ];
+    })
+  ];
+
+  mitmCache = gradle.fetchDeps {
+    inherit pname;
+    data = ./deps.json;
+  };
+
+  postPatch = ''
+    # Disable update check
+    substituteInPlace src/main/java/org/jabref/preferences/JabRefPreferences.java \
+      --replace 'VERSION_CHECK_ENABLED, Boolean.TRUE' \
+        'VERSION_CHECK_ENABLED, Boolean.FALSE'
+
+    # Find OpenOffice/LibreOffice binary
+    substituteInPlace src/main/java/org/jabref/logic/openoffice/OpenOfficePreferences.java \
+      --replace '/usr' '/run/current-system/sw'
+  '';
+
+  nativeBuildInputs = [
+    jdk
+    gradle
+    wrapGAppsHook3
+    copyDesktopItems
+    unzip
+  ];
+
+  buildInputs = [
+    gtk3
+    python3
+  ];
+
+  gradleFlags = [
+    "-PprojVersion=${version}"
+    "-Dorg.gradle.java.home=${jdk}"
+  ];
+
+  preBuild = ''
+    gradleFlagsArray+=(-PprojVersionInfo="${version} NixOS")
+  '';
+
+  dontWrapGApps = true;
+
+  installPhase = ''
+    runHook preInstall
+
+    install -dm755 $out/share/java/jabref
+    install -Dm644 LICENSE $out/share/licenses/jabref/LICENSE
+    install -Dm644 src/main/resources/icons/jabref.svg $out/share/pixmaps/jabref.svg
+
+    # script to support browser extensions
+    install -Dm755 buildres/linux/jabrefHost.py $out/lib/jabrefHost.py
+    patchShebangs $out/lib/jabrefHost.py
+    install -Dm644 buildres/linux/native-messaging-host/firefox/org.jabref.jabref.json $out/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json
+    sed -i -e "s|/opt/jabref|$out|" $out/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json
+
+    # Resources in the jar can't be found, workaround copied from AUR
+    cp -r build/resources $out/share/java/jabref
+
+    tar xf build/distributions/JabRef-${version}.tar -C $out --strip-components=1
+
+    DEFAULT_JVM_OPTS=$(sed -n -E "s/^DEFAULT_JVM_OPTS='(.*)'$/\1/p" $out/bin/JabRef | sed -e "s|\$APP_HOME|$out|g" -e 's/"//g')
+
+    # Temp fix: openjfx doesn't build with webkit
+    unzip $out/lib/javafx-web-*-*.jar libjfxwebkit.so -d $out/lib/
+
+    runHook postInstall
+  '';
+
+  postFixup = ''
+    rm $out/bin/*
+
+    # put this in postFixup because some gappsWrapperArgs are generated in gappsWrapperArgsHook in preFixup
+    makeWrapper ${jdk}/bin/java $out/bin/JabRef \
+      "''${gappsWrapperArgs[@]}" \
+      --suffix PATH : ${lib.makeBinPath [ xdg-utils ]} \
+      --add-flags "-Djava.library.path=$out/lib/ --patch-module org.jabref=$out/share/java/jabref/resources/main" \
+      --add-flags "$DEFAULT_JVM_OPTS"
+
+    # lowercase alias (for convenience and required for browser extensions)
+    ln -sf $out/bin/JabRef $out/bin/jabref
+  '';
+
+  gradleUpdateScript = ''
+    runHook preBuild
+
+    gradle nixDownloadDeps -Dos.arch=amd64
+    gradle nixDownloadDeps -Dos.arch=aarch64
+  '';
+
+  meta = with lib; {
+    description = "Open source bibliography reference manager";
+    homepage = "https://www.jabref.org";
+    sourceProvenance = with sourceTypes; [
+      fromSource
+      binaryBytecode # source bundles dependencies as jars
+      binaryNativeCode # source bundles dependencies as jars
+    ];
+    license = licenses.mit;
+    platforms = [
+      "x86_64-linux"
+      "aarch64-linux"
+    ];
+    maintainers = with maintainers; [
+      linsui
+    ];
+  };
+}

pkgs/by-name/ja/javaCup/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchurl,
+  ant,
+  jdk8,
+  makeWrapper,
+  stripJavaArchivesHook,
+}:
+let
+  jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "java-cup";
+  version = "11b-20160615";
+
+  src = fetchurl {
+    url = "http://www2.cs.tum.edu/projects/cup/releases/java-cup-src-${finalAttrs.version}.tar.gz";
+    hash = "sha256-4OdzYG5FzhqorROD5jk9U+2dzyhh5D76gZT1Z+kdv/o=";
+  };
+
+  sourceRoot = ".";
+
+  patches = [ ./javacup-0.11b_beta20160615-build-xml-git.patch ];
+
+  nativeBuildInputs = [
+    ant
+    jdk
+    makeWrapper
+    stripJavaArchivesHook
+  ];
+
+  buildPhase = ''
+    runHook preBuild
+    ant
+    runHook postBuild
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm644 dist/java-cup-11b.jar -t $out/share/java-cup
+    install -Dm644 dist/java-cup-11b-runtime.jar -t $out/share/java
+
+    makeWrapper ${jdk.jre}/bin/java $out/bin/javacup \
+        --add-flags "-jar $out/share/java-cup/java-cup-11b.jar"
+
+    runHook postInstall
+  '';
+
+  meta = {
+    description = "LALR parser generator for Java";
+    homepage = "http://www2.cs.tum.edu/projects/cup/";
+    license = lib.licenses.mit;
+    mainProgram = "javacup";
+    maintainers = [ lib.maintainers.romildo ];
+    platforms = lib.platforms.all;
+  };
+})

pkgs/by-name/ja/javacc/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  ant,
+  jdk8,
+  jre8,
+  makeWrapper,
+  stripJavaArchivesHook,
+}:
+let
+  # Upstream doesn't support anything newer than Java 8.
+  # https://github.com/javacc/javacc/blob/c708628423b71ce8bc3b70143fa5b6a2b7362b3a/README.md#building-javacc-from-source
+  jdk = jdk8;
+  jre = jre8;
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "javacc";
+  version = "7.0.13";
+
+  src = fetchFromGitHub {
+    owner = "javacc";
+    repo = "javacc";
+    rev = "javacc-${finalAttrs.version}";
+    hash = "sha256-nDJvKIbJc23Tvfn7Zqvt5tDDffNf4KQ0juGQQCZ+i1c=";
+  };
+
+  nativeBuildInputs = [
+    ant
+    jdk
+    makeWrapper
+    stripJavaArchivesHook
+  ];
+
+  buildPhase = ''
+    runHook preBuild
+    ant jar
+    runHook postBuild
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm644 target/javacc.jar -t $out/target
+    install -Dm755 scripts/{javacc,jjdoc,jjtree,jjrun} -t $out/bin
+
+    for file in $out/bin/*; do
+      wrapProgram "$file" --suffix PATH : ${jre}/bin
+    done
+
+    runHook postInstall
+  '';
+
+  doCheck = true;
+
+  checkPhase = ''
+    runHook preCheck
+    ant test
+    runHook postCheck
+  '';
+
+  meta = with lib; {
+    changelog = "https://github.com/javacc/javacc/blob/${finalAttrs.src.rev}/docs/release-notes.md";
+    description = "Parser generator for building parsers from grammars";
+    homepage = "https://javacc.github.io/javacc";
+    license = licenses.bsd2;
+    mainProgram = "javacc";
+    teams = [ teams.deshaw ];
+  };
+})

pkgs/by-name/ji/jing-trang/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  jre_headless,
+  jdk8_headless,
+  ant,
+  saxon,
+}:
+let
+  jdk_headless = jdk8_headless; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+in
+stdenv.mkDerivation rec {
+  pname = "jing-trang";
+  version = "20181222";
+
+  src = fetchFromGitHub {
+    owner = "relaxng";
+    repo = "jing-trang";
+    rev = "V${version}";
+    hash = "sha256-Krupa3MGk5UaaQsaNpPMZuIUzHJytDiksz9ysCPkFS4=";
+    fetchSubmodules = true;
+  };
+
+  buildInputs = [
+    jdk_headless
+    ant
+    saxon
+  ];
+
+  CLASSPATH = "lib/saxon.jar";
+
+  patches = [
+    ./no-git-during-build.patch
+  ];
+
+  preBuild = "ant";
+
+  installPhase = ''
+    mkdir -p "$out"/{share/java,bin}
+    cp ./build/*.jar ./lib/resolver.jar "$out/share/java/"
+
+    for tool in jing trang; do
+    cat > "$out/bin/$tool" <<EOF
+    #! $SHELL
+    export JAVA_HOME='${jre_headless}'
+    exec '${jre_headless}/bin/java' -jar '$out/share/java/$tool.jar' "\$@"
+    EOF
+    done
+
+    chmod +x "$out"/bin/*
+  '';
+
+  doCheck = true;
+  checkPhase = "ant test";
+
+  meta = with lib; {
+    description = "RELAX NG validator in Java";
+    # The homepage is www.thaiopensource.com, but it links to googlecode.com
+    # for downloads and call it the "project site".
+    homepage = "https://www.thaiopensource.com/relaxng/trang.html";
+    platforms = platforms.unix;
+    sourceProvenance = with sourceTypes; [
+      fromSource
+      binaryBytecode # source bundles dependencies as jars
+    ];
+    maintainers = [ maintainers.bjornfor ];
+  };
+}

pkgs/by-name/jp/jprofiler/package.nix

···
+{
+  stdenv,
+  lib,
+  fetchurl,
+  makeWrapper,
+  makeDesktopItem,
+  copyDesktopItems,
+  _7zz,
+  jdk11,
+}:
+
+let
+  jdk = jdk11;
+  pname = "jprofiler";
+  version = "14.0.5";
+  nameApp = "JProfiler";
+
+  meta = {
+    description = "Java profiler for deep JVM analysis";
+    longDescription = ''
+      JProfiler bridges high-level analytics and low-level JVM data,
+      delivering unmatched insights to solve your toughest performance
+      problems, memory leaks, threading issues, and higher-level problems in
+      technologies like JDBC, JPA, and more.
+    '';
+    homepage = "https://www.ej-technologies.com/products/jprofiler/overview.html";
+    license = lib.licenses.unfree;
+    maintainers = [ ];
+  };
+
+  src =
+    if stdenv.hostPlatform.isLinux then
+      fetchurl {
+        url = "https://download.ej-technologies.com/jprofiler/jprofiler_linux_${
+          lib.replaceStrings [ "." ] [ "_" ] version
+        }.tar.gz";
+        hash = "sha256-S7e2WurDJ0ePzpMg0YK94Mn0eHfb8/jNmf0kYts2Y0M=";
+      }
+    else
+      fetchurl {
+        url = "https://download-gcdn.ej-technologies.com/jprofiler/jprofiler_macos_${
+          lib.replaceStrings [ "." ] [ "_" ] version
+        }.dmg";
+        hash = "sha256-HPGh+dRfLuQprpgnu8oFboHUB1xvFqPblJcowqgZ5KA=";
+      };
+
+  desktopItems = [
+    (makeDesktopItem {
+      name = pname;
+      exec = pname;
+      icon = pname;
+      comment = meta.description;
+      desktopName = nameApp;
+      genericName = "Java Profiler Tool";
+      categories = [ "Development" ];
+    })
+  ];
+
+  linux = stdenv.mkDerivation {
+    inherit
+      pname
+      version
+      src
+      desktopItems
+      ;
+
+    nativeBuildInputs = [
+      makeWrapper
+      copyDesktopItems
+    ];
+
+    installPhase = ''
+      runHook preInstall
+
+      cp -r . $out
+
+      rm -f $out/bin/updater
+      rm -rf $out/bin/linux-ppc*
+      rm -rf $out/bin/linux-armhf
+      rm -rf $out/bin/linux-musl*
+
+      for f in $(find $out/bin -type f -executable); do
+        wrapProgram $f --set JAVA_HOME "${jdk.home}"
+      done
+
+      install -Dm644 "./.install4j/i4j_extf_7_1u09tly_16qtnph.png" \
+        "$out/share/icons/hicolor/scalable/apps/jprofiler.png"
+
+      runHook postInstall
+    '';
+
+    meta = meta // {
+      platforms = lib.platforms.linux;
+    };
+  };
+
+  darwin = stdenv.mkDerivation {
+    inherit pname version src;
+
+    nativeBuildInputs = [
+      makeWrapper
+      _7zz
+    ];
+
+    unpackPhase = ''
+      runHook preUnpack
+
+      7zz x $src -x!JProfiler/\[\]
+
+      runHook postUnpack
+    '';
+
+    sourceRoot = nameApp;
+
+    installPhase = ''
+      runHook preInstall
+
+      mkdir -p $out/{Applications,bin}
+      cp -R ${nameApp}.app $out/Applications/
+      makeWrapper $out/Applications/${nameApp}.app/Contents/MacOS/JavaApplicationStub $out/bin/${pname}
+
+      runHook postInstall
+    '';
+
+    meta = meta // {
+      platforms = lib.platforms.darwin;
+    };
+  };
+in
+if stdenv.hostPlatform.isDarwin then darwin else linux

pkgs/by-name/ke/keystore-explorer/package.nix

···
+{
+  fetchzip,
+  lib,
+  stdenv,
+  jdk11,
+  runtimeShell,
+  glib,
+  wrapGAppsHook3,
+}:
+let
+  jdk = jdk11;
+in
+stdenv.mkDerivation rec {
+  version = "5.6.0";
+  pname = "keystore-explorer";
+  src = fetchzip {
+    url = "https://github.com/kaikramer/keystore-explorer/releases/download/v${version}/kse-${
+      lib.replaceStrings [ "." ] [ "" ] version
+    }.zip";
+    sha256 = "sha256-+ZgALJaZodLmAtdCIE1SG6D0lzlETg4mMPXheXmGhPc=";
+  };
+
+  # glib is necessary so file dialogs don't hang.
+  buildInputs = [ glib ];
+  nativeBuildInputs = [ wrapGAppsHook3 ];
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/bin
+    mkdir -p $out/share/keystore-explorer
+    cp -R icons licenses lib kse.jar $out/share/keystore-explorer/
+
+    # keystore-explorer's kse.sh tries to detect the path of Java by using
+    # Python on Darwin; just write our own start script to avoid unnecessary dependencies
+    cat > $out/bin/keystore-explorer <<EOF
+    #!${runtimeShell}
+    export JAVA_HOME=${jdk.home}
+    exec ${jdk}/bin/java -jar $out/share/keystore-explorer/kse.jar "\$@"
+    EOF
+    chmod +x $out/bin/keystore-explorer
+
+    runHook postInstall
+  '';
+
+  dontStrip = true;
+  dontBuild = true;
+  dontConfigure = true;
+
+  meta = {
+    description = "Open source GUI replacement for the Java command-line utilities keytool and jarsigner";
+    mainProgram = "keystore-explorer";
+    sourceProvenance = with lib.sourceTypes; [ binaryBytecode ];
+    license = lib.licenses.gpl3Only;
+    maintainers = [ lib.maintainers.numinit ];
+    platforms = lib.platforms.unix;
+  };
+}

pkgs/by-name/li/libmatthew_java/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchurl,
+  jdk8,
+}:
+let
+  jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+in
+stdenv.mkDerivation rec {
+  pname = "libmatthew-java";
+  version = "0.8";
+
+  src = fetchurl {
+    url = "https://src.fedoraproject.org/repo/pkgs/libmatthew-java/libmatthew-java-${version}.tar.gz/8455b8751083ce25c99c2840609271f5/libmatthew-java-${version}.tar.gz";
+    sha256 = "1yldkhsdzm0a41a0i881bin2jklhp85y3ah245jd6fz3npcx7l85";
+  };
+  JAVA_HOME = jdk;
+  PREFIX = "\${out}";
+  buildInputs = [ jdk ];
+
+  meta = with lib; {
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sander ];
+    license = licenses.mit;
+  };
+}

pkgs/by-name/mc/mcaselector/package.nix

···
+{
+  lib,
+  stdenvNoCC,
+  fetchurl,
+  makeWrapper,
+  wrapGAppsHook3,
+  jre,
+}:
+let
+  jre' = jre.override {
+    enableJavaFX = true;
+  };
+in
+stdenvNoCC.mkDerivation (finalAttrs: {
+  pname = "mcaselector";
+  version = "2.5.3";
+
+  src = fetchurl {
+    url = "https://github.com/Querz/mcaselector/releases/download/${finalAttrs.version}/mcaselector-${finalAttrs.version}.jar";
+    hash = "sha256-PQCXwtEK+Tq1cRJDkzlQ43dhdQ3J+bd8x/ymvsfIfdA=";
+  };
+
+  dontUnpack = true;
+  dontBuild = true;
+
+  nativeBuildInputs = [
+    jre'
+    makeWrapper
+    wrapGAppsHook3
+  ];
+
+  dontWrapGApps = true;
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/{bin,lib/mcaselector}
+    cp $src $out/lib/mcaselector/mcaselector.jar
+
+    runHook postInstall
+  '';
+
+  preFixup = ''
+    makeWrapper ${jre'}/bin/java $out/bin/mcaselector \
+      --add-flags "-jar $out/lib/mcaselector/mcaselector.jar" \
+      ''${gappsWrapperArgs[@]}
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/Querz/mcaselector";
+    description = "Tool to select chunks from Minecraft worlds for deletion or export";
+    mainProgram = "mcaselector";
+    sourceProvenance = with sourceTypes; [ binaryBytecode ];
+    license = licenses.mit;
+    maintainers = [ maintainers.Scrumplex ];
+    platforms = platforms.linux;
+  };
+})

pkgs/by-name/op/openapi-generator-cli/package.nix

···
+{
+  callPackage,
+  lib,
+  stdenv,
+  fetchurl,
+  jre_headless,
+  makeWrapper,
+}:
+
+let
+  jre = jre_headless;
+  this = stdenv.mkDerivation (finalAttrs: {
+    version = "7.15.0";
+    pname = "openapi-generator-cli";
+
+    jarfilename = "openapi-generator-cli-${finalAttrs.version}.jar";
+
+    nativeBuildInputs = [
+      makeWrapper
+    ];
+
+    src = fetchurl {
+      url = "mirror://maven/org/openapitools/openapi-generator-cli/${finalAttrs.version}/${finalAttrs.jarfilename}";
+      sha256 = "sha256-TaGnzbeMOkOx6rBkiJETXow1R9Lu26Ddadrzd/hl82Y=";
+    };
+
+    dontUnpack = true;
+
+    installPhase = ''
+      runHook preInstall
+
+      install -D "$src" "$out/share/java/${finalAttrs.jarfilename}"
+
+      makeWrapper ${jre}/bin/java $out/bin/${finalAttrs.pname} \
+        --add-flags "-jar $out/share/java/${finalAttrs.jarfilename}"
+
+      runHook postInstall
+    '';
+
+    meta = with lib; {
+      description = "Allows generation of API client libraries (SDK generation), server stubs and documentation automatically given an OpenAPI Spec";
+      homepage = "https://github.com/OpenAPITools/openapi-generator";
+      changelog = "https://github.com/OpenAPITools/openapi-generator/releases/tag/v${finalAttrs.version}";
+      sourceProvenance = with sourceTypes; [ binaryBytecode ];
+      license = licenses.asl20;
+      maintainers = with maintainers; [ shou ];
+      mainProgram = "openapi-generator-cli";
+    };
+
+    passthru.tests.example = callPackage ./example.nix {
+      openapi-generator-cli = this;
+    };
+  });
+in
+this

pkgs/by-name/op/openrefine/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  buildNpmPackage,
+  curl,
+  jdk17,
+  jq,
+  makeWrapper,
+  maven,
+}:
+
+let
+  jdk = jdk17;
+  version = "3.9.5";
+  src = fetchFromGitHub {
+    owner = "openrefine";
+    repo = "openrefine";
+    rev = version;
+    hash = "sha256-548vOJf0mlk1AuuMjEXpsiVjft6UbJrUxh5mSca8Xbw=";
+  };
+
+  npmPkg = buildNpmPackage {
+    inherit src version;
+
+    pname = "openrefine-npm";
+    sourceRoot = "${src.name}/main/webapp";
+
+    npmDepsHash = "sha256-I0iqGniXeqyCWf1DG2nMNkTScCrtJYeYF9n2Zt6Syjc=";
+
+    # package.json doesn't supply a version, which npm doesn't like - fix this.
+    # directly referencing jq because buildNpmPackage doesn't pass
+    # nativeBuildInputs through to fetchNpmDeps
+    postPatch = ''
+      NEW_PACKAGE_JSON=$(mktemp)
+      ${jq}/bin/jq '. + {version: $ENV.version}' package.json > $NEW_PACKAGE_JSON
+      cp $NEW_PACKAGE_JSON package.json
+    '';
+
+    dontNpmBuild = true;
+    installPhase = ''
+      mkdir -p $out
+      cp -r modules/core/3rdparty/* $out/
+    '';
+  };
+
+in
+maven.buildMavenPackage {
+  inherit src version;
+
+  pname = "openrefine";
+
+  postPatch = ''
+    cp -r ${npmPkg} main/webapp/modules/core/3rdparty
+  '';
+
+  mvnJdk = jdk;
+  mvnParameters = "-pl !packaging";
+  mvnHash = "sha256-SV5nfyUeyRul/YfZZXor8O37ARdCtKkrHCLzQrmr96s=";
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  doCheck = false;
+
+  installPhase = ''
+    mkdir -p $out/lib/server/target/lib
+    cp -r server/target/lib/* $out/lib/server/target/lib/
+    cp server/target/openrefine-*-server.jar $out/lib/server/target/lib/
+
+    mkdir -p $out/lib/webapp
+    cp -r main/webapp/{WEB-INF,modules} $out/lib/webapp/
+    (
+      cd extensions
+      for ext in * ; do
+        if [ -d "$ext/module" ] ; then
+          mkdir -p "$out/lib/webapp/extensions/$ext"
+          cp -r "$ext/module" "$out/lib/webapp/extensions/$ext/"
+        fi
+      done
+    )
+
+    mkdir -p $out/etc
+    cp refine.ini $out/etc/
+
+    mkdir -p $out/bin
+    cp refine $out/bin/
+  '';
+
+  preFixup = ''
+    find $out -name '*.java' -delete
+    sed -i -E 's|^(butterfly\.modules\.path =).*extensions.*$|\1 '"$out/lib/webapp/extensions|" \
+      $out/lib/webapp/WEB-INF/butterfly.properties
+
+    sed -i 's|^cd `dirname \$0`$|cd '"$out/lib|" $out/bin/refine
+
+    cat >> $out/etc/refine.ini <<EOF
+    REFINE_WEBAPP='$out/lib/webapp'
+    REFINE_LIB_DIR='$out/lib/server/target/lib'
+
+    JAVA_HOME='${jdk.home}'
+
+    # non-headless mode tries to launch a browser, causing a
+    # number of purity problems
+    JAVA_OPTIONS='-Drefine.headless=true'
+    EOF
+
+    wrapProgram $out/bin/refine \
+      --prefix PATH : '${
+        lib.makeBinPath [
+          jdk
+          curl
+        ]
+      }' \
+      --set-default REFINE_INI_PATH "$out/etc/refine.ini"
+  '';
+
+  passthru = {
+    inherit npmPkg;
+    updateScript = ./update.sh;
+  };
+
+  meta = with lib; {
+    description = "Power tool for working with messy data and improving it";
+    homepage = "https://openrefine.org";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [
+      ris
+      arcstur
+    ];
+    sourceProvenance = with sourceTypes; [
+      fromSource
+      binaryBytecode # maven dependencies
+    ];
+    broken = stdenv.hostPlatform.isDarwin; # builds, doesn't run
+    mainProgram = "refine";
+  };
+}

pkgs/by-name/pa/pattypan/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  ant,
+  jdk,
+  makeWrapper,
+  wrapGAppsHook3,
+  makeDesktopItem,
+  copyDesktopItems,
+  stripJavaArchivesHook,
+}:
+let
+  jdk' = jdk.override { enableJavaFX = true; };
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "pattypan";
+  version = "22.03";
+
+  src = fetchFromGitHub {
+    owner = "yarl";
+    repo = "pattypan";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-wMQrBg+rEV1W7NgtWFXZr3pAxpyqdbEBKLNwDDGju2I=";
+  };
+
+  nativeBuildInputs = [
+    ant
+    jdk
+    makeWrapper
+    wrapGAppsHook3
+    copyDesktopItems
+    stripJavaArchivesHook
+  ];
+
+  dontWrapGApps = true;
+
+  env.JAVA_TOOL_OPTIONS = "-Dfile.encoding=UTF8"; # needed for jdk versions below jdk19
+
+  buildPhase = ''
+    runHook preBuild
+    ant
+    runHook postBuild
+  '';
+
+  installPhase = ''
+    runHook preInstall
+    install -Dm644 pattypan.jar -t $out/share/pattypan
+    install -Dm644 src/pattypan/resources/logo.png $out/share/pixmaps/pattypan.png
+    runHook postInstall
+  '';
+
+  # gappsWrapperArgs is set in preFixup
+  postFixup = ''
+    makeWrapper ${jdk'}/bin/java $out/bin/pattypan \
+        ''${gappsWrapperArgs[@]} \
+        --add-flags "-jar $out/share/pattypan/pattypan.jar"
+  '';
+
+  desktopItems = [
+    (makeDesktopItem {
+      name = "pattypan";
+      exec = "pattypan";
+      icon = "pattypan";
+      desktopName = "Pattypan";
+      genericName = "An uploader for Wikimedia Commons";
+      categories = [ "Utility" ];
+    })
+  ];
+
+  meta = with lib; {
+    description = "Uploader for Wikimedia Commons";
+    homepage = "https://commons.wikimedia.org/wiki/Commons:Pattypan";
+    license = licenses.mit;
+    mainProgram = "pattypan";
+    maintainers = with maintainers; [ fee1-dead ];
+    platforms = platforms.all;
+    sourceProvenance = with sourceTypes; [
+      fromSource
+      binaryBytecode # source bundles dependencies as jars
+    ];
+  };
+})

pkgs/by-name/pr/processing/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchurl,
+  ant,
+  unzip,
+  makeWrapper,
+  jdk17,
+  jogl,
+  rsync,
+  ffmpeg,
+  batik,
+  stripJavaArchivesHook,
+  wrapGAppsHook3,
+  libGL,
+}:
+let
+  jdk = jdk17;
+  buildNumber = "1295";
+  vaqua = fetchurl {
+    name = "VAqua9.jar";
+    url = "https://violetlib.org/release/vaqua/9/VAqua9.jar";
+    sha256 = "cd0b82df8e7434c902ec873364bf3e9a3e6bef8b59cbf42433130d71bf1a779c";
+  };
+
+  jna = fetchurl {
+    name = "jna-5.10.0.zip";
+    url = "https://github.com/java-native-access/jna/archive/5.10.0.zip";
+    sha256 = "B5CakOQ8225xNsk2TMV8CbK3RcsLlb+pHzjaY5JNwg0=";
+  };
+
+  flatlaf = fetchurl {
+    name = "flatlaf-2.4.jar";
+    url = "mirror://maven/com/formdev/flatlaf/2.4/flatlaf-2.4.jar";
+    sha256 = "NVMYiCd+koNCJ6X3EiRx1Aj+T5uAMSJ9juMmB5Os+zc=";
+  };
+
+  lsp4j = fetchurl {
+    name = "org.eclipse.lsp4j-0.19.0.jar";
+    url = "mirror://maven/org/eclipse/lsp4j/org.eclipse.lsp4j/0.19.0/org.eclipse.lsp4j-0.19.0.jar";
+    sha256 = "sha256-1DI5D9KW+GL4gT1qjwVZveOl5KVOEjt6uXDwsFzi8Sg=";
+  };
+
+  lsp4j-jsonrpc = fetchurl {
+    name = "org.eclipse.lsp4j.jsonrpc-0.19.0.jar";
+    url = "mirror://maven/org/eclipse/lsp4j/org.eclipse.lsp4j.jsonrpc/0.19.0/org.eclipse.lsp4j.jsonrpc-0.19.0.jar";
+    sha256 = "sha256-ozYTkvv7k0psCeX/PbSM3/Bl17qT3upX3trt65lmM9I=";
+  };
+
+  gson = fetchurl {
+    name = "gson-2.9.1.jar";
+    url = "mirror://maven/com/google/code/gson/gson/2.9.1/gson-2.9.1.jar";
+    sha256 = "sha256-N4U04znm5tULFzb7Ort28cFdG+P0wTzsbVNkEuI9pgM=";
+  };
+
+  arch =
+    {
+      x86_64 = "amd64";
+    }
+    .${stdenv.hostPlatform.parsed.cpu.name} or stdenv.hostPlatform.parsed.cpu.name;
+in
+stdenv.mkDerivation rec {
+  pname = "processing";
+  version = "4.3.2";
+
+  src = fetchFromGitHub {
+    owner = "processing";
+    repo = "processing4";
+    rev = "processing-${buildNumber}-${version}";
+    sha256 = "sha256-jUkWnkP8up5vpaXfgFJ/jQjN1KfeX5EuYXSb+W6NEms=";
+  };
+
+  # Processing did not update the todo.txt file before tagging this release, so
+  # the "revision-check" Ant target fails.
+  patches = [ ./disable-revision-check.patch ];
+
+  nativeBuildInputs = [
+    ant
+    unzip
+    makeWrapper
+    stripJavaArchivesHook
+    wrapGAppsHook3
+  ];
+  buildInputs = [
+    jdk
+    jogl
+    ant
+    rsync
+    ffmpeg
+    batik
+  ];
+
+  dontWrapGApps = true;
+
+  buildPhase = ''
+    runHook preBuild
+
+    echo "tarring jdk"
+    tar --checkpoint=10000 -czf build/linux/jdk-17.0.8-${arch}.tgz ${jdk}
+    cp ${ant.home}/lib/{ant.jar,ant-launcher.jar} app/lib/
+    mkdir -p core/library
+    ln -s ${jogl}/share/java/* core/library/
+    ln -s ${vaqua} app/lib/VAqua9.jar
+    ln -s ${flatlaf} app/lib/flatlaf.jar
+    ln -s ${lsp4j} java/mode/org.eclipse.lsp4j.jar
+    ln -s ${lsp4j-jsonrpc} java/mode/org.eclipse.lsp4j.jsonrpc.jar
+    ln -s ${gson} java/mode/gson.jar
+    unzip -qo ${jna} -d app/lib/
+    mv app/lib/{jna-5.10.0/dist/jna.jar,}
+    mv app/lib/{jna-5.10.0/dist/jna-platform.jar,}
+    ln -sf ${batik}/* java/libraries/svg/library/
+    cp java/libraries/svg/library/share/java/batik-all-${batik.version}.jar java/libraries/svg/library/batik.jar
+    echo "tarring ffmpeg"
+    tar --checkpoint=10000 -czf build/shared/tools/MovieMaker/ffmpeg-5.0.1.gz ${ffmpeg}
+    cd build
+    ant build
+    cd ..
+
+    runHook postBuild
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/share/
+    mkdir -p $out/share/applications/
+    cp -dp build/linux/${pname}.desktop $out/share/applications/
+    cp -dpr build/linux/work $out/share/${pname}
+    rmdir $out/share/${pname}/java
+    ln -s ${jdk} $out/share/${pname}/java
+    makeWrapper $out/share/${pname}/processing $out/bin/processing \
+      ''${gappsWrapperArgs[@]} \
+      --prefix LD_LIBRARY_PATH : "${lib.makeLibraryPath [ libGL ]}" \
+      --prefix _JAVA_OPTIONS " " "-Dawt.useSystemAAFontSettings=gasp"
+    makeWrapper $out/share/${pname}/processing-java $out/bin/processing-java \
+      ''${gappsWrapperArgs[@]} \
+      --prefix LD_LIBRARY_PATH : "${lib.makeLibraryPath [ libGL ]}" \
+      --prefix _JAVA_OPTIONS " " "-Dawt.useSystemAAFontSettings=gasp"
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Language and IDE for electronic arts";
+    homepage = "https://processing.org";
+    license = with licenses; [
+      gpl2Only
+      lgpl21Only
+    ];
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ evan-goode ];
+  };
+}

pkgs/by-name/sc/scalafix/package.nix

···
+{
+  lib,
+  stdenv,
+  jre8,
+  coursier,
+  makeWrapper,
+  installShellFiles,
+  setJavaClassPath,
+  testers,
+}:
+let
+  jre = jre8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "scalafix";
+  version = "0.12.0";
+  deps = stdenv.mkDerivation {
+    name = "${finalAttrs.pname}-deps-${finalAttrs.version}";
+    buildCommand = ''
+      export COURSIER_CACHE=$(pwd)
+      ${coursier}/bin/cs fetch ch.epfl.scala:scalafix-cli_2.13.13:${finalAttrs.version} > deps
+      mkdir -p $out/share/java
+      cp $(< deps) $out/share/java/
+    '';
+    outputHashMode = "recursive";
+    outputHash = "sha256-HMTnr3awTIAgLSl4eF36U1kv162ajJxC5MreSk2TfUE=";
+  };
+
+  nativeBuildInputs = [
+    makeWrapper
+    installShellFiles
+    setJavaClassPath
+  ];
+  buildInputs = [ finalAttrs.deps ];
+
+  dontUnpack = true;
+
+  installPhase = ''
+    makeWrapper ${jre}/bin/java $out/bin/${finalAttrs.pname} \
+      --add-flags "-cp $CLASSPATH scalafix.cli.Cli"
+
+    installShellCompletion --cmd ${finalAttrs.pname} \
+      --bash <($out/bin/${finalAttrs.pname} --bash) \
+      --zsh  <($out/bin/${finalAttrs.pname} --zsh)
+  '';
+
+  passthru.tests = {
+    testVersion = testers.testVersion {
+      package = finalAttrs.finalPackage;
+      version = "${finalAttrs.version}";
+    };
+  };
+
+  meta = with lib; {
+    description = "Refactoring and linting tool for Scala";
+    mainProgram = "scalafix";
+    homepage = "https://scalacenter.github.io/scalafix/";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.tomahna ];
+    sourceProvenance = with sourceTypes; [ binaryBytecode ];
+  };
+})

pkgs/by-name/sl/slipstream/package.nix

···
+{
+  lib,
+  fetchFromGitHub,
+  makeWrapper,
+  maven,
+  jdk8,
+}:
+let
+  jdk = jdk8;
+in
+maven.buildMavenPackage rec {
+  pname = "slipstream";
+  version = "1.9.1";
+
+  src = fetchFromGitHub {
+    owner = "Vhati";
+    repo = "Slipstream-Mod-Manager";
+    rev = "v${version}";
+    hash = "sha256-F+o94Oh9qxVdfgwdmyOv+WZl1BjQuzhQWaVrAgScgIU=";
+  };
+
+  mvnJdk = jdk;
+  mvnHash = "sha256-woOSkF5TuzaJ84EndryMoXTMbbK/V/BShM1k+WB8D/c=";
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/share/java
+    install -Dm644 target/ftl-mod-manager-${version}.jar $out/share/java
+    install -Dm644 target/modman.jar $out/share/java
+
+    # slipstream is very finniky about having specific
+    # folders at startup, so wrapper creates them for it.
+    # this is because slipstream expects to be started from
+    # archive it comes from, but we can't do that since
+    # we need the mods directory to be writable.
+    # see: https://github.com/Vhati/Slipstream-Mod-Manager/blob/85cad4ffbef8583d908b189204d7d22a26be43f8/src/main/java/net/vhati/modmanager/cli/SlipstreamCLI.java#L105
+    makeWrapper ${jdk}/bin/java $out/bin/${pname} \
+      --run '_dir="''${XDG_DATA_HOME:-$HOME/.local/share}/slipstream"' \
+      --run 'mkdir -p $_dir/{mods,backup}' \
+      --run 'cd $_dir' \
+      --append-flags "-jar $out/share/java/modman.jar"
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Mod manager for FTL: Faster Than Light";
+    homepage = "https://github.com/Vhati/Slipstream-Mod-Manager";
+    license = licenses.gpl2Only;
+    maintainers = with maintainers; [ mib ];
+    mainProgram = "slipstream";
+  };
+}

pkgs/by-name/tr/trimmomatic/package.nix

···
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  ant,
+  jdk21_headless,
+  jre_minimal,
+  makeWrapper,
+  stripJavaArchivesHook,
+}:
+let
+  jdk = jdk21_headless;
+  # Reduce closure size
+  jre = jre_minimal.override {
+    modules = [
+      "java.base"
+      "java.logging"
+    ];
+    jdk = jdk21_headless;
+  };
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "trimmomatic";
+  version = "0.39";
+
+  src = fetchFromGitHub {
+    owner = "usadellab";
+    repo = "Trimmomatic";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-u+ubmacwPy/vsEi0YQCv0fTnVDesQvqeQDEwCbS8M6I=";
+  };
+
+  # Remove jdk version requirement
+  postPatch = ''
+    substituteInPlace ./build.xml \
+      --replace 'source="1.5" target="1.5"' ""
+  '';
+
+  nativeBuildInputs = [
+    ant
+    jdk
+    makeWrapper
+    stripJavaArchivesHook
+  ];
+
+  buildPhase = ''
+    runHook preBuild
+
+    ant
+
+    runHook postBuild
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm644 dist/jar/trimmomatic-*.jar -t $out/share/trimmomatic
+    cp -r adapters $out/share/trimmomatic
+
+    makeWrapper ${jre}/bin/java $out/bin/trimmomatic \
+        --add-flags "-jar $out/share/trimmomatic/trimmomatic-*.jar"
+
+    runHook postInstall
+  '';
+
+  meta = {
+    changelog = "https://github.com/usadellab/Trimmomatic/blob/main/versionHistory.txt";
+    description = "Flexible read trimming tool for Illumina NGS data";
+    longDescription = ''
+      Trimmomatic performs a variety of useful trimming tasks for illumina
+      paired-end and single ended data: adapter trimming, quality trimming,
+      cropping to a specified length, length filtering, quality score
+      conversion.
+    '';
+    homepage = "http://www.usadellab.org/cms/?page=trimmomatic";
+    downloadPage = "https://github.com/usadellab/Trimmomatic/releases";
+    license = lib.licenses.gpl3Only;
+    sourceProvenance = [
+      lib.sourceTypes.fromSource
+      lib.sourceTypes.binaryBytecode # source bundles dependencies as jars
+    ];
+    mainProgram = "trimmomatic";
+    maintainers = [ lib.maintainers.kupac ];
+  };
+})

pkgs/by-name/xm/xmloscopy/package.nix

···
   coreutils,
   libxml2,
   libxslt,
-  jing,
+  jing-trang,
   findutils,
   gnugrep,
   gnused,
···
     coreutils
     libxml2
     libxslt
-    jing
+    jing-trang
     findutils
     gnugrep
     gnused

pkgs/by-name/yo/yourkit-java/package.nix

···
   copyDesktopItems,
   imagemagick,
   makeDesktopItem,
-  jre,
+  jdk21,
 }:
 let
+  jre = jdk21;
+
   vPath = v: lib.elemAt (lib.splitString "-" v) 0;
 
   version = "2025.3-b154";

pkgs/development/compilers/abcl/default.nix

···
   writeShellScriptBin,
   fetchurl,
   ant,
-  jdk,
+  openjdk17,
   makeWrapper,
   stripJavaArchivesHook,
 }:
 
 let
+  # https://armedbear.common-lisp.dev/ lists OpenJDK 17 as the highest
+  # supported JDK.
+  jdk = openjdk17;
+
   fakeHostname = writeShellScriptBin "hostname" ''
     echo nix-builder.localdomain
   '';

pkgs/development/compilers/adoptopenjdk-icedtea-web/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  cargo,
-  rustc,
-  autoreconfHook,
-  jdk,
-  glib,
-  firefox-unwrapped,
-  zip,
-  pkg-config,
-  npapi_sdk,
-  bash,
-  bc,
-}:
-
-stdenv.mkDerivation rec {
-  pname = "adoptopenjdk-icedtea-web";
-
-  version = "1.8.8";
-
-  src = fetchFromGitHub {
-    owner = "AdoptOpenJDK";
-    repo = "IcedTea-Web";
-    rev = "icedtea-web-${version}";
-    sha256 = "sha256-hpEVWG9ltNDL/0EFJjgQRRce+BLcCO4ZERULYZxyC1o=";
-  };
-
-  nativeBuildInputs = [
-    autoreconfHook
-    pkg-config
-    bc
-  ];
-  buildInputs = [
-    cargo
-    rustc
-    glib
-    firefox-unwrapped
-    zip
-    npapi_sdk
-  ];
-
-  preConfigure = ''
-    configureFlagsArray+=("BIN_BASH=${bash}/bin/bash")
-  '';
-
-  patches = [ ./patches/0001-make-cargo-work-with-nix-build-on-linux.patch ];
-
-  doCheck = true;
-  preCheck = ''
-    # Needed for the below rust-launcher tests to pass
-    # dirs_paths_helper::tests::check_config_files_paths
-    # dirs_paths_helper::tests::check_legacy_config_files_paths
-
-    mkdir -p $HOME/.icedtea
-    touch $HOME/.icedtea/deployment.properties
-
-    mkdir -p $XDG_CONFIG_HOME/icedtea-web
-    touch $XDG_CONFIG_HOME/icedtea-web/deployment.properties
-  '';
-
-  HOME = "/build";
-  XDG_CONFIG_HOME = "/build";
-
-  configureFlags = [
-    "--with-itw-libs=DISTRIBUTION"
-    "--with-jdk-home=${jdk.home}"
-    "--disable-docs"
-  ];
-
-  mozillaPlugin = "/lib";
-
-  postInstall = ''
-    mkdir -p $out/share/applications
-    cp javaws.desktop itweb-settings.desktop policyeditor.desktop $out/share/applications
-  '';
-
-  meta = {
-    description = "Java web browser plugin and an implementation of Java Web Start";
-    longDescription = ''
-      A Free Software web browser plugin running applets written in the Java
-      programming language and an implementation of Java Web Start, originally
-      based on the NetX project.
-    '';
-    homepage = "https://github.com/adoptopenjdk/icedtea-web";
-    platforms = lib.platforms.linux;
-  };
-}

pkgs/development/compilers/ballerina/default.nix

···
-{
-  ballerina,
-  lib,
-  writeText,
-  runCommand,
-  makeWrapper,
-  fetchzip,
-  stdenv,
-  openjdk,
-}:
-let
-  version = "2201.10.3";
-  codeName = "swan-lake";
-in
-stdenv.mkDerivation {
-  pname = "ballerina";
-  inherit version;
-
-  src = fetchzip {
-    url = "https://dist.ballerina.io/downloads/${version}/ballerina-${version}-${codeName}.zip";
-    hash = "sha256-JVwxWRiOQaUZBkvxoLhKvktyQYnBtbCBZXZa6g6hoRQ=";
-  };
-
-  nativeBuildInputs = [ makeWrapper ];
-
-  installPhase = ''
-    runHook preInstall
-    cp -rv distributions/ballerina-${version} $out
-    runHook postInstall
-  '';
-  preFixup = ''
-    wrapProgram $out/bin/bal --set JAVA_HOME ${openjdk}
-  '';
-
-  passthru.tests.smokeTest =
-    let
-      helloWorld = writeText "hello-world.bal" ''
-        import ballerina/io;
-        public function main() {
-          io:println("Hello, World!");
-        }
-      '';
-    in
-    runCommand "ballerina-${version}-smoketest" { } ''
-      ${ballerina}/bin/bal run ${helloWorld} >$out
-      read result <$out
-      [[ $result = "Hello, World!" ]]
-    '';
-
-  meta = with lib; {
-    description = "Open-source programming language for the cloud";
-    mainProgram = "bal";
-    license = licenses.asl20;
-    platforms = openjdk.meta.platforms;
-    maintainers = with maintainers; [ eigengrau ];
-    sourceProvenance = with sourceTypes; [ binaryBytecode ];
-  };
-}

pkgs/development/interpreters/clojure/default.nix

···
   bashNonInteractive,
   fetchurl,
   installShellFiles,
-  jdk,
+  jdk21,
   rlwrap,
   makeWrapper,
   writeScript,
 }:
-
+let
+  # set this to an LTS version of java
+  jdk = jdk21;
+in
 stdenv.mkDerivation (finalAttrs: {
   pname = "clojure";
   version = "1.12.2.1565";

pkgs/development/libraries/java/cup/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchurl,
-  ant,
-  jdk,
-  makeWrapper,
-  stripJavaArchivesHook,
-}:
-
-stdenv.mkDerivation (finalAttrs: {
-  pname = "java-cup";
-  version = "11b-20160615";
-
-  src = fetchurl {
-    url = "http://www2.cs.tum.edu/projects/cup/releases/java-cup-src-${finalAttrs.version}.tar.gz";
-    hash = "sha256-4OdzYG5FzhqorROD5jk9U+2dzyhh5D76gZT1Z+kdv/o=";
-  };
-
-  sourceRoot = ".";
-
-  patches = [ ./javacup-0.11b_beta20160615-build-xml-git.patch ];
-
-  nativeBuildInputs = [
-    ant
-    jdk
-    makeWrapper
-    stripJavaArchivesHook
-  ];
-
-  buildPhase = ''
-    runHook preBuild
-    ant
-    runHook postBuild
-  '';
-
-  installPhase = ''
-    runHook preInstall
-
-    install -Dm644 dist/java-cup-11b.jar -t $out/share/java-cup
-    install -Dm644 dist/java-cup-11b-runtime.jar -t $out/share/java
-
-    makeWrapper ${jdk.jre}/bin/java $out/bin/javacup \
-        --add-flags "-jar $out/share/java-cup/java-cup-11b.jar"
-
-    runHook postInstall
-  '';
-
-  meta = {
-    description = "LALR parser generator for Java";
-    homepage = "http://www2.cs.tum.edu/projects/cup/";
-    license = lib.licenses.mit;
-    mainProgram = "javacup";
-    maintainers = [ lib.maintainers.romildo ];
-    platforms = lib.platforms.all;
-  };
-})

pkgs/development/libraries/java/libmatthew-java/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchurl,
-  jdk,
-}:
-
-stdenv.mkDerivation rec {
-  pname = "libmatthew-java";
-  version = "0.8";
-
-  src = fetchurl {
-    url = "https://src.fedoraproject.org/repo/pkgs/libmatthew-java/libmatthew-java-${version}.tar.gz/8455b8751083ce25c99c2840609271f5/libmatthew-java-${version}.tar.gz";
-    sha256 = "1yldkhsdzm0a41a0i881bin2jklhp85y3ah245jd6fz3npcx7l85";
-  };
-  JAVA_HOME = jdk;
-  PREFIX = "\${out}";
-  buildInputs = [ jdk ];
-
-  meta = with lib; {
-    platforms = platforms.linux;
-    maintainers = [ maintainers.sander ];
-    license = licenses.mit;
-  };
-}

pkgs/development/tools/java/jprofiler/default.nix

···
-{
-  stdenv,
-  lib,
-  fetchurl,
-  makeWrapper,
-  makeDesktopItem,
-  copyDesktopItems,
-  _7zz,
-  jdk,
-}:
-
-let
-  pname = "jprofiler";
-  version = "14.0.5";
-  nameApp = "JProfiler";
-
-  meta = {
-    description = "Java profiler for deep JVM analysis";
-    longDescription = ''
-      JProfiler bridges high-level analytics and low-level JVM data,
-      delivering unmatched insights to solve your toughest performance
-      problems, memory leaks, threading issues, and higher-level problems in
-      technologies like JDBC, JPA, and more.
-    '';
-    homepage = "https://www.ej-technologies.com/products/jprofiler/overview.html";
-    license = lib.licenses.unfree;
-    maintainers = [ ];
-  };
-
-  src =
-    if stdenv.hostPlatform.isLinux then
-      fetchurl {
-        url = "https://download.ej-technologies.com/jprofiler/jprofiler_linux_${
-          lib.replaceStrings [ "." ] [ "_" ] version
-        }.tar.gz";
-        hash = "sha256-S7e2WurDJ0ePzpMg0YK94Mn0eHfb8/jNmf0kYts2Y0M=";
-      }
-    else
-      fetchurl {
-        url = "https://download-gcdn.ej-technologies.com/jprofiler/jprofiler_macos_${
-          lib.replaceStrings [ "." ] [ "_" ] version
-        }.dmg";
-        hash = "sha256-HPGh+dRfLuQprpgnu8oFboHUB1xvFqPblJcowqgZ5KA=";
-      };
-
-  desktopItems = [
-    (makeDesktopItem {
-      name = pname;
-      exec = pname;
-      icon = pname;
-      comment = meta.description;
-      desktopName = nameApp;
-      genericName = "Java Profiler Tool";
-      categories = [ "Development" ];
-    })
-  ];
-
-  linux = stdenv.mkDerivation {
-    inherit
-      pname
-      version
-      src
-      desktopItems
-      ;
-
-    nativeBuildInputs = [
-      makeWrapper
-      copyDesktopItems
-    ];
-
-    installPhase = ''
-      runHook preInstall
-
-      cp -r . $out
-
-      rm -f $out/bin/updater
-      rm -rf $out/bin/linux-ppc*
-      rm -rf $out/bin/linux-armhf
-      rm -rf $out/bin/linux-musl*
-
-      for f in $(find $out/bin -type f -executable); do
-        wrapProgram $f --set JAVA_HOME "${jdk.home}"
-      done
-
-      install -Dm644 "./.install4j/i4j_extf_7_1u09tly_16qtnph.png" \
-        "$out/share/icons/hicolor/scalable/apps/jprofiler.png"
-
-      runHook postInstall
-    '';
-
-    meta = meta // {
-      platforms = lib.platforms.linux;
-    };
-  };
-
-  darwin = stdenv.mkDerivation {
-    inherit pname version src;
-
-    nativeBuildInputs = [
-      makeWrapper
-      _7zz
-    ];
-
-    unpackPhase = ''
-      runHook preUnpack
-
-      7zz x $src -x!JProfiler/\[\]
-
-      runHook postUnpack
-    '';
-
-    sourceRoot = nameApp;
-
-    installPhase = ''
-      runHook preInstall
-
-      mkdir -p $out/{Applications,bin}
-      cp -R ${nameApp}.app $out/Applications/
-      makeWrapper $out/Applications/${nameApp}.app/Contents/MacOS/JavaApplicationStub $out/bin/${pname}
-
-      runHook postInstall
-    '';
-
-    meta = meta // {
-      platforms = lib.platforms.darwin;
-    };
-  };
-in
-if stdenv.hostPlatform.isDarwin then darwin else linux

pkgs/development/tools/parsing/javacc/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  ant,
-  jdk,
-  jre,
-  makeWrapper,
-  stripJavaArchivesHook,
-}:
-
-stdenv.mkDerivation (finalAttrs: {
-  pname = "javacc";
-  version = "7.0.13";
-
-  src = fetchFromGitHub {
-    owner = "javacc";
-    repo = "javacc";
-    rev = "javacc-${finalAttrs.version}";
-    hash = "sha256-nDJvKIbJc23Tvfn7Zqvt5tDDffNf4KQ0juGQQCZ+i1c=";
-  };
-
-  nativeBuildInputs = [
-    ant
-    jdk
-    makeWrapper
-    stripJavaArchivesHook
-  ];
-
-  buildPhase = ''
-    runHook preBuild
-    ant jar
-    runHook postBuild
-  '';
-
-  installPhase = ''
-    runHook preInstall
-
-    install -Dm644 target/javacc.jar -t $out/target
-    install -Dm755 scripts/{javacc,jjdoc,jjtree,jjrun} -t $out/bin
-
-    for file in $out/bin/*; do
-      wrapProgram "$file" --suffix PATH : ${jre}/bin
-    done
-
-    runHook postInstall
-  '';
-
-  doCheck = true;
-
-  checkPhase = ''
-    runHook preCheck
-    ant test
-    runHook postCheck
-  '';
-
-  meta = with lib; {
-    changelog = "https://github.com/javacc/javacc/blob/${finalAttrs.src.rev}/docs/release-notes.md";
-    description = "Parser generator for building parsers from grammars";
-    homepage = "https://javacc.github.io/javacc";
-    license = licenses.bsd2;
-    mainProgram = "javacc";
-    teams = [ teams.deshaw ];
-  };
-})

pkgs/development/tools/scalafix/default.nix

···
-{
-  lib,
-  stdenv,
-  jre,
-  coursier,
-  makeWrapper,
-  installShellFiles,
-  setJavaClassPath,
-  testers,
-}:
-stdenv.mkDerivation (finalAttrs: {
-  pname = "scalafix";
-  version = "0.12.0";
-  deps = stdenv.mkDerivation {
-    name = "${finalAttrs.pname}-deps-${finalAttrs.version}";
-    buildCommand = ''
-      export COURSIER_CACHE=$(pwd)
-      ${coursier}/bin/cs fetch ch.epfl.scala:scalafix-cli_2.13.13:${finalAttrs.version} > deps
-      mkdir -p $out/share/java
-      cp $(< deps) $out/share/java/
-    '';
-    outputHashMode = "recursive";
-    outputHash = "sha256-HMTnr3awTIAgLSl4eF36U1kv162ajJxC5MreSk2TfUE=";
-  };
-
-  nativeBuildInputs = [
-    makeWrapper
-    installShellFiles
-    setJavaClassPath
-  ];
-  buildInputs = [ finalAttrs.deps ];
-
-  dontUnpack = true;
-
-  installPhase = ''
-    makeWrapper ${jre}/bin/java $out/bin/${finalAttrs.pname} \
-      --add-flags "-cp $CLASSPATH scalafix.cli.Cli"
-
-    installShellCompletion --cmd ${finalAttrs.pname} \
-      --bash <($out/bin/${finalAttrs.pname} --bash) \
-      --zsh  <($out/bin/${finalAttrs.pname} --zsh)
-  '';
-
-  passthru.tests = {
-    testVersion = testers.testVersion {
-      package = finalAttrs.finalPackage;
-      version = "${finalAttrs.version}";
-    };
-  };
-
-  meta = with lib; {
-    description = "Refactoring and linting tool for Scala";
-    mainProgram = "scalafix";
-    homepage = "https://scalacenter.github.io/scalafix/";
-    license = licenses.bsd3;
-    maintainers = [ maintainers.tomahna ];
-    sourceProvenance = with sourceTypes; [ binaryBytecode ];
-  };
-})

pkgs/servers/elasticmq-server-bin/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchurl,
-  jdk,
-  jre,
-  makeBinaryWrapper,
-  runCommand,
-  python3Packages,
-  writeText,
-}:
-
-stdenv.mkDerivation (finalAttrs: {
-  pname = "elasticmq-server";
-  version = "1.6.14";
-
-  src = fetchurl {
-    url = "https://s3-eu-west-1.amazonaws.com/softwaremill-public/elasticmq-server-${finalAttrs.version}.jar";
-    sha256 = "sha256-HVllLHz6zutonaLFwgyQKYSZxfp5QMslxf/PlzGWyG4=";
-  };
-
-  # don't do anything?
-  unpackPhase = "${jdk}/bin/jar xf $src favicon.png";
-
-  nativeBuildInputs = [ makeBinaryWrapper ];
-
-  installPhase = ''
-    mkdir -p $out/bin $out/share/elasticmq-server
-
-    cp $src $out/share/elasticmq-server/elasticmq-server.jar
-
-    # TODO: how to add extraArgs? current workaround is to use JAVA_TOOL_OPTIONS environment to specify properties
-    makeWrapper ${jre}/bin/java $out/bin/elasticmq-server \
-      --add-flags "-jar $out/share/elasticmq-server/elasticmq-server.jar"
-  '';
-
-  passthru.tests.elasticmqTest = import ./elasticmq-test.nix {
-    inherit runCommand python3Packages writeText;
-    elasticmq-server = finalAttrs.finalPackage;
-  };
-
-  meta = with lib; {
-    description = "Message queueing system with Java, Scala and Amazon SQS-compatible interfaces";
-    homepage = "https://github.com/softwaremill/elasticmq";
-    changelog = "https://github.com/softwaremill/elasticmq/releases/tag/v${finalAttrs.version}";
-    sourceProvenance = with sourceTypes; [ binaryBytecode ];
-    license = licenses.asl20;
-    platforms = platforms.unix;
-    maintainers = with maintainers; [ peterromfeldhk ];
-    mainProgram = "elasticmq-server";
-  };
-})

pkgs/tools/games/minecraft/mcaselector/default.nix

···
-{
-  lib,
-  stdenvNoCC,
-  fetchurl,
-  makeWrapper,
-  wrapGAppsHook3,
-  jre,
-}:
-
-stdenvNoCC.mkDerivation (finalAttrs: {
-  pname = "mcaselector";
-  version = "2.5.3";
-
-  src = fetchurl {
-    url = "https://github.com/Querz/mcaselector/releases/download/${finalAttrs.version}/mcaselector-${finalAttrs.version}.jar";
-    hash = "sha256-PQCXwtEK+Tq1cRJDkzlQ43dhdQ3J+bd8x/ymvsfIfdA=";
-  };
-
-  dontUnpack = true;
-  dontBuild = true;
-
-  nativeBuildInputs = [
-    jre
-    makeWrapper
-    wrapGAppsHook3
-  ];
-
-  dontWrapGApps = true;
-
-  installPhase = ''
-    runHook preInstall
-
-    mkdir -p $out/{bin,lib/mcaselector}
-    cp $src $out/lib/mcaselector/mcaselector.jar
-
-    runHook postInstall
-  '';
-
-  preFixup = ''
-    makeWrapper ${jre}/bin/java $out/bin/mcaselector \
-      --add-flags "-jar $out/lib/mcaselector/mcaselector.jar" \
-      ''${gappsWrapperArgs[@]}
-  '';
-
-  meta = with lib; {
-    homepage = "https://github.com/Querz/mcaselector";
-    description = "Tool to select chunks from Minecraft worlds for deletion or export";
-    mainProgram = "mcaselector";
-    sourceProvenance = with sourceTypes; [ binaryBytecode ];
-    license = licenses.mit;
-    maintainers = [ maintainers.Scrumplex ];
-    platforms = platforms.linux;
-  };
-})

pkgs/tools/games/slipstream/default.nix

···
-{
-  lib,
-  fetchFromGitHub,
-  makeWrapper,
-  maven,
-  jdk,
-}:
-
-maven.buildMavenPackage rec {
-  pname = "slipstream";
-  version = "1.9.1";
-
-  src = fetchFromGitHub {
-    owner = "Vhati";
-    repo = "Slipstream-Mod-Manager";
-    rev = "v${version}";
-    hash = "sha256-F+o94Oh9qxVdfgwdmyOv+WZl1BjQuzhQWaVrAgScgIU=";
-  };
-
-  mvnJdk = jdk;
-  mvnHash = "sha256-woOSkF5TuzaJ84EndryMoXTMbbK/V/BShM1k+WB8D/c=";
-
-  nativeBuildInputs = [ makeWrapper ];
-
-  installPhase = ''
-    runHook preInstall
-
-    mkdir -p $out/share/java
-    install -Dm644 target/ftl-mod-manager-${version}.jar $out/share/java
-    install -Dm644 target/modman.jar $out/share/java
-
-    # slipstream is very finniky about having specific
-    # folders at startup, so wrapper creates them for it.
-    # this is because slipstream expects to be started from
-    # archive it comes from, but we can't do that since
-    # we need the mods directory to be writable.
-    # see: https://github.com/Vhati/Slipstream-Mod-Manager/blob/85cad4ffbef8583d908b189204d7d22a26be43f8/src/main/java/net/vhati/modmanager/cli/SlipstreamCLI.java#L105
-    makeWrapper ${jdk}/bin/java $out/bin/${pname} \
-      --run '_dir="''${XDG_DATA_HOME:-$HOME/.local/share}/slipstream"' \
-      --run 'mkdir -p $_dir/{mods,backup}' \
-      --run 'cd $_dir' \
-      --append-flags "-jar $out/share/java/modman.jar"
-
-    runHook postInstall
-  '';
-
-  meta = with lib; {
-    description = "Mod manager for FTL: Faster Than Light";
-    homepage = "https://github.com/Vhati/Slipstream-Mod-Manager";
-    license = licenses.gpl2Only;
-    maintainers = with maintainers; [ mib ];
-    mainProgram = "slipstream";
-  };
-}

pkgs/tools/networking/openapi-generator-cli/default.nix

···
-{
-  callPackage,
-  lib,
-  stdenv,
-  fetchurl,
-  jre,
-  makeWrapper,
-}:
-
-let
-  this = stdenv.mkDerivation (finalAttrs: {
-    version = "7.15.0";
-    pname = "openapi-generator-cli";
-
-    jarfilename = "openapi-generator-cli-${finalAttrs.version}.jar";
-
-    nativeBuildInputs = [
-      makeWrapper
-    ];
-
-    src = fetchurl {
-      url = "mirror://maven/org/openapitools/openapi-generator-cli/${finalAttrs.version}/${finalAttrs.jarfilename}";
-      sha256 = "sha256-TaGnzbeMOkOx6rBkiJETXow1R9Lu26Ddadrzd/hl82Y=";
-    };
-
-    dontUnpack = true;
-
-    installPhase = ''
-      runHook preInstall
-
-      install -D "$src" "$out/share/java/${finalAttrs.jarfilename}"
-
-      makeWrapper ${jre}/bin/java $out/bin/${finalAttrs.pname} \
-        --add-flags "-jar $out/share/java/${finalAttrs.jarfilename}"
-
-      runHook postInstall
-    '';
-
-    meta = with lib; {
-      description = "Allows generation of API client libraries (SDK generation), server stubs and documentation automatically given an OpenAPI Spec";
-      homepage = "https://github.com/OpenAPITools/openapi-generator";
-      changelog = "https://github.com/OpenAPITools/openapi-generator/releases/tag/v${finalAttrs.version}";
-      sourceProvenance = with sourceTypes; [ binaryBytecode ];
-      license = licenses.asl20;
-      maintainers = with maintainers; [ shou ];
-      mainProgram = "openapi-generator-cli";
-    };
-
-    passthru.tests.example = callPackage ./example.nix {
-      openapi-generator-cli = this;
-    };
-  });
-in
-this

pkgs/tools/package-management/disnix/DisnixWebService/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  fetchpatch,
-  ant,
-  jdk,
-  xmlstarlet,
-  axis2,
-  dbus_java,
-}:
-
-stdenv.mkDerivation (finalAttrs: {
-  pname = "DisnixWebService";
-  version = "0.10.1";
-
-  src = fetchFromGitHub {
-    owner = "svanderburg";
-    repo = "DisnixWebService";
-    rev = "DisnixWebService-${finalAttrs.version}";
-    hash = "sha256-zcYr2Ytx4pevSthTQLpnQ330wDxN9dWsZA20jbO6PxQ=";
-  };
-
-  patches = [
-    # Correct the DisnixWebService build for compatibility with Axis2 1.8.1
-    # See https://github.com/svanderburg/DisnixWebService/pull/2
-    (fetchpatch {
-      url = "https://github.com/svanderburg/DisnixWebService/commit/cee99c6af744b5dda16728a70ebd2800f61871a0.patch";
-      hash = "sha256-4rSEN8AwivUXUCIUYFBRIoE19jVDv+Vpgakmy8fR06A=";
-    })
-  ];
-
-  nativeBuildInputs = [
-    ant
-    jdk
-    xmlstarlet
-  ];
-
-  env = {
-    PREFIX = "\${env.out}";
-    AXIS2_LIB = "${axis2}/lib";
-    AXIS2_WEBAPP = "${axis2}/webapps/axis2";
-    DBUS_JAVA_LIB = "${dbus_java}/share/java";
-  };
-
-  prePatch = ''
-    # add modificationtime="0" to the <jar> and <war> tasks to achieve reproducibility
-    xmlstarlet ed -L -a "//jar|//war" -t attr -n "modificationtime" -v "0" build.xml
-
-    sed -i -e "s|#JAVA_HOME=|JAVA_HOME=${jdk}|" \
-       -e "s|#AXIS2_LIB=|AXIS2_LIB=${axis2}/lib|" \
-        scripts/disnix-soap-client
-  '';
-
-  buildPhase = ''
-    runHook preBuild
-    ant
-    runHook postBuild
-  '';
-
-  installPhase = ''
-    runHook preInstall
-    ant install
-    runHook postInstall
-  '';
-
-  meta = {
-    description = "SOAP interface and client for Disnix";
-    mainProgram = "disnix-soap-client";
-    homepage = "https://github.com/svanderburg/DisnixWebService";
-    changelog = "https://github.com/svanderburg/DisnixWebService/blob/${finalAttrs.src.rev}/NEWS.txt";
-    license = lib.licenses.mit;
-    maintainers = [ lib.maintainers.sander ];
-    platforms = lib.platforms.linux;
-  };
-})

pkgs/tools/text/xml/jing-trang/default.nix

···
-{
-  lib,
-  stdenv,
-  fetchFromGitHub,
-  jre_headless,
-  jdk_headless,
-  ant,
-  saxon,
-}:
-
-stdenv.mkDerivation rec {
-  pname = "jing-trang";
-  version = "20181222";
-
-  src = fetchFromGitHub {
-    owner = "relaxng";
-    repo = "jing-trang";
-    rev = "V${version}";
-    hash = "sha256-Krupa3MGk5UaaQsaNpPMZuIUzHJytDiksz9ysCPkFS4=";
-    fetchSubmodules = true;
-  };
-
-  buildInputs = [
-    jdk_headless
-    ant
-    saxon
-  ];
-
-  CLASSPATH = "lib/saxon.jar";
-
-  patches = [
-    ./no-git-during-build.patch
-  ];
-
-  preBuild = "ant";
-
-  installPhase = ''
-    mkdir -p "$out"/{share/java,bin}
-    cp ./build/*.jar ./lib/resolver.jar "$out/share/java/"
-
-    for tool in jing trang; do
-    cat > "$out/bin/$tool" <<EOF
-    #! $SHELL
-    export JAVA_HOME='${jre_headless}'
-    exec '${jre_headless}/bin/java' -jar '$out/share/java/$tool.jar' "\$@"
-    EOF
-    done
-
-    chmod +x "$out"/bin/*
-  '';
-
-  doCheck = true;
-  checkPhase = "ant test";
-
-  meta = with lib; {
-    description = "RELAX NG validator in Java";
-    # The homepage is www.thaiopensource.com, but it links to googlecode.com
-    # for downloads and call it the "project site".
-    homepage = "https://www.thaiopensource.com/relaxng/trang.html";
-    platforms = platforms.unix;
-    sourceProvenance = with sourceTypes; [
-      fromSource
-      binaryBytecode # source bundles dependencies as jars
-    ];
-    maintainers = [ maintainers.bjornfor ];
-  };
-}

pkgs/top-level/aliases.nix

···
   jd-cli = throw "jd-cli has been removed due to upstream being unmaintained since 2019. Other Java decompilers in Nixpkgs include bytecode-viewer (GUI), cfr (CLI), and procyon (CLI)."; # Added 2024-10-30
   jd-gui = throw "jd-gui has been removed due to a dependency on the dead JCenter Bintray. Other Java decompilers in Nixpkgs include bytecode-viewer (GUI), cfr (CLI), and procyon (CLI)."; # Added 2024-10-30
   jikespg = throw "'jikespg' has been removed due to lack of maintenance upstream."; # Added 2025-06-10
+  jing = jing-trang; # Added 2025-09-18
   jsawk = throw "'jsawk' has been removed because it is unmaintained upstream"; # Added 2024-08-07
   jscoverage = throw "jscoverage has been removed, as it was broken"; # Added 2025-08-25
 

pkgs/top-level/all-packages.nix

···
 
   makehuman = libsForQt5.callPackage ../applications/misc/makehuman { };
 
-  mcaselector = callPackage ../tools/games/minecraft/mcaselector {
-    jre = jre.override {
-      enableJavaFX = true;
-    };
-  };
-
   mkosi = callPackage ../tools/virtualization/mkosi { };
 
   mkosi-full = mkosi.override { withQemu = true; };
···
   sdkmanager = with python3Packages; toPythonApplication sdkmanager;
 
   shaperglot = with python3Packages; toPythonApplication shaperglot;
-
-  slipstream = callPackage ../tools/games/slipstream {
-    jdk = jdk8;
-  };
 
   supermin = callPackage ../tools/virtualization/supermin {
     ocamlPackages = ocaml-ng.ocamlPackages_4_14;
···
   go2tv-lite = go2tv.override { withGui = false; };
 
   guglielmo = libsForQt5.callPackage ../applications/radio/guglielmo { };
-
-  gremlin-console = callPackage ../applications/misc/gremlin-console {
-    openjdk = openjdk11;
-  };
-
-  gremlin-server = callPackage ../applications/misc/gremlin-server {
-    openjdk = openjdk11;
-  };
 
   hinit = haskell.lib.compose.justStaticExecutables haskellPackages.hinit;
 
···
 
   jello = with python3Packages; toPythonApplication jello;
 
-  jing = res.jing-trang;
-  jing-trang = callPackage ../tools/text/xml/jing-trang {
-    jdk_headless = jdk8_headless; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
-
   jl = haskellPackages.jl;
 
   joplin = nodePackages.joplin;
···
   kbfs = callPackage ../tools/security/keybase/kbfs.nix { };
 
   keybase-gui = callPackage ../tools/security/keybase/gui.nix { };
-
-  keystore-explorer = callPackage ../applications/misc/keystore-explorer {
-    jdk = jdk11;
-  };
 
   kio-fuse = libsForQt5.callPackage ../tools/filesystems/kio-fuse { };
 
···
 
   onlykey = callPackage ../tools/security/onlykey { node_webkit = nwjs; };
 
-  openapi-generator-cli = callPackage ../tools/networking/openapi-generator-cli {
-    jre = pkgs.jre_headless;
-  };
-
   ophcrack-cli = ophcrack.override { enableGui = false; };
 
   open-interpreter = with python3Packages; toPythonApplication open-interpreter;
···
     privsepUser = "ntp";
     privsepPath = "/var/empty";
   };
-
-  openrefine = callPackage ../applications/science/misc/openrefine { jdk = jdk17; };
 
   openrgb-with-all-plugins = openrgb.withPlugins [
     openrgb-plugin-effects
···
 
   snapcast = callPackage ../applications/audio/snapcast {
     pulseaudioSupport = config.pulseaudio or stdenv.hostPlatform.isLinux;
-  };
-
-  soapui = callPackage ../applications/networking/soapui {
-    jdk = jdk11;
   };
 
   specup = haskellPackages.specup.bin;
···
   adaptivecppWithCuda = adaptivecpp.override { cudaSupport = true; };
   adaptivecppWithRocm = adaptivecpp.override { rocmSupport = true; };
 
-  adoptopenjdk-icedtea-web = callPackage ../development/compilers/adoptopenjdk-icedtea-web {
-    jdk = jdk8;
-  };
-
   armips = callPackage ../by-name/ar/armips/package.nix {
     stdenv = clangStdenv;
-  };
-
-  ballerina = callPackage ../development/compilers/ballerina {
-    openjdk = openjdk17_headless;
   };
 
   binaryen = callPackage ../development/compilers/binaryen {
···
     coursier = coursier.override { jre = jdk8; };
   };
 
-  scalafix = callPackage ../development/tools/scalafix {
-    jre = jre8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
   # smlnjBootstrap should be redundant, now that smlnj works on Darwin natively
   smlnjBootstrap = callPackage ../development/compilers/smlnj/bootstrap.nix { };
   smlnj = callPackage ../development/compilers/smlnj { };
···
     xeus-cling
     ;
 
-  clojure = callPackage ../development/interpreters/clojure {
-    # set this to an LTS version of java
-    jdk = jdk21;
-  };
+  clojure = callPackage ../development/interpreters/clojure { };
 
   clooj = callPackage ../development/interpreters/clojure/clooj.nix { };
 
···
   janet = callPackage ../development/interpreters/janet { };
 
   jpm = callPackage ../development/interpreters/janet/jpm.nix { };
-
-  davmail = callPackage ../applications/networking/davmail {
-    jre = jdk11.override { enableJavaFX = true; };
-    zulu = zulu11.override { enableJavaFX = true; };
-  };
 
   lambda-lisp-blc = lambda-lisp;
 
···
     inochi-session
     ;
 
-  javacc = callPackage ../development/tools/parsing/javacc {
-    # Upstream doesn't support anything newer than Java 8.
-    # https://github.com/javacc/javacc/blob/c708628423b71ce8bc3b70143fa5b6a2b7362b3a/README.md#building-javacc-from-source
-    jdk = jdk8;
-    jre = jre8;
-  };
-
   jenkins-job-builder = with python3Packages; toPythonApplication jenkins-job-builder;
 
   kustomize = callPackage ../development/tools/kustomize { };
···
 
   gdbHostCpuOnly = gdb.override { hostCpuOnly = true; };
 
-  jprofiler = callPackage ../development/tools/java/jprofiler {
-    jdk = jdk11;
-  };
-
   valgrind-light = (valgrind.override { gdb = null; }).overrideAttrs (oldAttrs: {
     meta = oldAttrs.meta // {
       description = "${oldAttrs.meta.description} (without GDB)";
···
   xxdiff = libsForQt5.callPackage ../development/tools/misc/xxdiff { };
 
   xxdiff-tip = xxdiff;
-
-  yourkit-java = callPackage ../by-name/yo/yourkit-java/package.nix {
-    jre = jdk21;
-  };
 
   yq = python3.pkgs.toPythonApplication python3.pkgs.yq;
 
···
   malcontent = callPackage ../development/libraries/malcontent { };
 
   malcontent-ui = callPackage ../development/libraries/malcontent/ui.nix { };
-
-  libmatthew_java = callPackage ../development/libraries/java/libmatthew-java {
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
 
   inherit
     ({
···
 
   ### DEVELOPMENT / LIBRARIES / JAVA
 
-  javaCup = callPackage ../development/libraries/java/cup {
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
-
   saxonb = saxonb_8_8;
   saxon-he = saxon_12-he;
 
···
 
   # Armed Bear Common Lisp
   abcl = wrapLisp {
-    pkg = callPackage ../development/compilers/abcl {
-      # https://armedbear.common-lisp.dev/ lists OpenJDK 17 as the highest
-      # supported JDK.
-      jdk = openjdk17;
-    };
+    pkg = callPackage ../development/compilers/abcl { };
     faslExt = "abcl";
   };
 
···
 
   dodgy = with python3Packages; toPythonApplication dodgy;
 
-  envoy = callPackage ../by-name/en/envoy/package.nix {
-    jdk = openjdk11_headless;
-  };
-
   etcd = etcd_3_5;
   etcd_3_4 = callPackage ../servers/etcd/3_4 { };
   etcd_3_5 = callPackage ../servers/etcd/3_5 { };
···
   prosody = callPackage ../servers/xmpp/prosody {
     withExtraLibs = [ ];
     withExtraLuaPackages = _: [ ];
-  };
-
-  elasticmq-server-bin = callPackage ../servers/elasticmq-server-bin {
-    jre = jre8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
   };
 
   felix = callPackage ../servers/felix { };
···
 
   espeakedit = callPackage ../applications/audio/espeak/edit.nix { };
 
-  greenfoot = callPackage ../applications/editors/greenfoot {
-    openjdk = openjdk21.override {
-      enableJavaFX = true;
-      openjfx_jdk = openjfx21.override { withWebKit = true; };
-    };
-  };
-
   input-leap = qt6Packages.callPackage ../applications/misc/input-leap {
     avahi = avahi.override { withLibdnssdCompat = true; };
   };
···
   fritzing = qt6Packages.callPackage ../applications/science/electronics/fritzing { };
 
   fvwm = fvwm2;
-
-  ganttproject-bin = callPackage ../applications/misc/ganttproject-bin {
-    jre = openjdk17.override {
-      enableJavaFX = true;
-    };
-  };
 
   gaucheBootstrap = callPackage ../development/interpreters/gauche/boot.nix { };
 
···
   mindforger = libsForQt5.callPackage ../applications/editors/mindforger { };
 
   molsketch = libsForQt5.callPackage ../applications/editors/molsketch { };
-
-  pattypan = callPackage ../applications/misc/pattypan {
-    jdk = jdk.override { enableJavaFX = true; };
-  };
 
   gphoto2 = callPackage ../applications/misc/gphoto2 { };
 
···
 
   jabcode-reader = callPackage ../development/libraries/jabcode {
     subproject = "reader";
-  };
-
-  jabref = callPackage ../applications/office/jabref {
-    jdk = jdk21.override {
-      enableJavaFX = true;
-      openjfx_jdk = openjfx23;
-    };
   };
 
   jackmix = libsForQt5.callPackage ../applications/audio/jackmix { };
···
 
   qiv = callPackage ../applications/graphics/qiv {
     imlib2 = imlib2Full;
-  };
-
-  processing = callPackage ../applications/graphics/processing {
-    jdk = jdk17;
   };
 
   # perhaps there are better apps for this task? It's how I had configured my previous system.
···
 
   raxml-mpi = raxml.override { useMpi = true; };
 
-  trimmomatic = callPackage ../applications/science/biology/trimmomatic {
-    jdk = pkgs.jdk21_headless;
-    # Reduce closure size
-    jre = pkgs.jre_minimal.override {
-      modules = [
-        "java.base"
-        "java.logging"
-      ];
-      jdk = pkgs.jdk21_headless;
-    };
-  };
-
   ### SCIENCE/MACHINE LEARNING
 
   streamlit = with python3Packages; toPythonApplication streamlit;
···
       inherit (python3Packages) supervisor;
     }
   );
-
-  DisnixWebService = callPackage ../tools/package-management/disnix/DisnixWebService {
-    jdk = jdk8;
-  };
 
   lice = python3Packages.callPackage ../tools/misc/lice { };