diff --git a/beast-base/src/assembly/package.xml b/beast-base/src/assembly/package.xml
index f09968ba..3b01d986 100644
--- a/beast-base/src/assembly/package.xml
+++ b/beast-base/src/assembly/package.xml
@@ -3,10 +3,20 @@
           xsi:schemaLocation="http://maven.apache.org/ASSEMBLY/2.1.1 http://maven.apache.org/xsd/assembly-2.1.1.xsd">
     <!-- Builds the installable BEAST.base package zip:
            version.xml          (the BEAST.base package descriptor, at repo root)
+           BEAST.base.src.jar   the package sources, at the zip root (BEAST2 convention)
            lib/beast-base.jar    + its third-party runtime dependencies
+           examples/             example XML (+ nexus data) shown in BEAUti
          beast-pkgmgmt is excluded: it is the bootstrap/launcher and is always
          provided by the core distribution, so bundling it here would duplicate
-         the beast.pkgmgmt module on the module path. -->
+         the beast.pkgmgmt module on the module path.
+
+         Examples are shipped *inside the package* (not only in the release
+         bundle root) so that a BEAST.base point release can update them via the
+         package manager: seedBundledPackage()/the package manager extract them
+         to <user package dir>/BEAST.base/examples, which BeautiTabPane and
+         PackageHealthChecker discover by scanning getBeastDirectories(). The
+         curated subset mirrors what release/.../assemble-bundle.sh copies into
+         the bundle root. -->
     <id>package</id>
     <formats>
         <format>zip</format>
@@ -18,8 +28,29 @@
             <source>${project.basedir}/../version.xml</source>
             <outputDirectory>.</outputDirectory>
         </file>
+        <!-- Source jar at the zip root as BEAST.base.src.jar, matching the BEAST2
+             convention (<PackageName>.src.jar). The -sources.jar is built by
+             maven-source-plugin (jar-no-fork) in the same package phase, ordered
+             before the assembly execution so it exists when this runs. -->
+        <file>
+            <source>${project.build.directory}/${project.build.finalName}-sources.jar</source>
+            <outputDirectory>.</outputDirectory>
+            <destName>BEAST.base.src.jar</destName>
+        </file>
     </files>
 
+    <fileSets>
+        <fileSet>
+            <directory>${project.basedir}/src/test/resources/beast.base/examples</directory>
+            <outputDirectory>examples</outputDirectory>
+            <includes>
+                <include>*.xml</include>
+                <include>spec/*.xml</include>
+                <include>nexus/**</include>
+            </includes>
+        </fileSet>
+    </fileSets>
+
     <dependencySets>
         <dependencySet>
             <outputDirectory>lib</outputDirectory>
diff --git a/beast-base/src/main/java/beast/base/minimal/BeastMain.java b/beast-base/src/main/java/beast/base/minimal/BeastMain.java
index a4cb8d3f..1598c22a 100644
--- a/beast-base/src/main/java/beast/base/minimal/BeastMain.java
+++ b/beast-base/src/main/java/beast/base/minimal/BeastMain.java
@@ -69,6 +69,12 @@ public static void printUsage(final Arguments arguments) {
 	private static void printVersion() {
     	Log.info("BEAST " + (new BEASTVersion()).getVersionString());
         Log.info("---");
+        // The same package can be discovered through more than one directory on
+        // the package path (e.g. BEAST.base is found both in the user package dir
+        // and via the bundle-root version.xml). List each package once, noting
+        // where it was found; later duplicates are reported as skipped, but only
+        // in verbose mode.
+        java.util.Set<String> printed = new java.util.HashSet<>();
         for (String jarDirName : PackageManager.getBeastDirectories()) {
             File versionFile = new File(jarDirName + "/version.xml");
             if (versionFile.exists()) {
@@ -77,9 +83,14 @@ private static void printVersion() {
 	                DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
 	                Document doc = factory.newDocumentBuilder().parse(versionFile);
 	                Element packageElement = doc.getDocumentElement();
-	                Log.info.print(packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version"));
-	                Log.debug.print(" " + jarDirName);
-	                Log.info.print("\n");
+	                String nameAndVersion = packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version");
+	                if (printed.add(nameAndVersion)) {
+	                	Log.info.print(nameAndVersion);
+	                	Log.debug.print(" (found in " + jarDirName + ")");
+	                	Log.info.print("\n");
+	                } else {
+	                	Log.debug.println("Skipping duplicate " + nameAndVersion + " found in " + jarDirName);
+	                }
             	} catch (IOException| SAXException| ParserConfigurationException e) {
             		Log.err(e.getMessage());
             	}
diff --git a/beast-fx/src/assembly/package.xml b/beast-fx/src/assembly/package.xml
index bdba2ffc..fc55e178 100644
--- a/beast-fx/src/assembly/package.xml
+++ b/beast-fx/src/assembly/package.xml
@@ -3,6 +3,7 @@
           xsi:schemaLocation="http://maven.apache.org/ASSEMBLY/2.1.1 http://maven.apache.org/xsd/assembly-2.1.1.xsd">
     <!-- Builds the installable BEAST.app package zip:
            version.xml          (the BEAST.app package descriptor)
+           BEAST.app.src.jar    the package sources, at the zip root (BEAST2 convention)
            lib/beast-fx.jar
          Only beast-fx.jar is bundled. Its dependencies are provided at runtime:
          beast-base (the BEAST.base package), beast-pkgmgmt (the bootstrap), and
@@ -26,6 +27,15 @@
             <source>${project.basedir}/version.xml</source>
             <outputDirectory>.</outputDirectory>
         </file>
+        <!-- Source jar at the zip root as BEAST.app.src.jar, matching the BEAST2
+             convention (<PackageName>.src.jar). The -sources.jar is built by
+             maven-source-plugin (jar-no-fork) in the same package phase, ordered
+             before the assembly execution so it exists when this runs. -->
+        <file>
+            <source>${project.build.directory}/${project.build.finalName}-sources.jar</source>
+            <outputDirectory>.</outputDirectory>
+            <destName>BEAST.app.src.jar</destName>
+        </file>
     </files>
 
     <dependencySets>
diff --git a/beast-fx/src/main/java/beastfx/app/beast/BeastMain.java b/beast-fx/src/main/java/beastfx/app/beast/BeastMain.java
index f87be3f8..1324fb38 100644
--- a/beast-fx/src/main/java/beastfx/app/beast/BeastMain.java
+++ b/beast-fx/src/main/java/beastfx/app/beast/BeastMain.java
@@ -103,6 +103,12 @@ public static void printUsage(final Arguments arguments) {
 	private static void printVersion() {
     	Log.info("BEAST " + (new BEASTVersion()).getVersionString());
         Log.info("---");
+        // The same package can be discovered through more than one directory on
+        // the package path (e.g. BEAST.base is found both in the user package dir
+        // and via the bundle-root version.xml). List each package once, noting
+        // where it was found; later duplicates are reported as skipped, but only
+        // in verbose mode.
+        java.util.Set<String> printed = new java.util.HashSet<>();
         for (String jarDirName : PackageManager.getBeastDirectories()) {
             File versionFile = new File(jarDirName + "/version.xml");
             if (versionFile.exists()) {
@@ -111,9 +117,14 @@ private static void printVersion() {
 	                DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
 	                Document doc = factory.newDocumentBuilder().parse(versionFile);
 	                Element packageElement = doc.getDocumentElement();
-	                Log.info.print(packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version"));
-	                Log.debug.print(" " + jarDirName);
-	                Log.info.print("\n");
+	                String nameAndVersion = packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version");
+	                if (printed.add(nameAndVersion)) {
+	                	Log.info.print(nameAndVersion);
+	                	Log.debug.print(" (found in " + jarDirName + ")");
+	                	Log.info.print("\n");
+	                } else {
+	                	Log.debug.println("Skipping duplicate " + nameAndVersion + " found in " + jarDirName);
+	                }
             	} catch (IOException| SAXException| ParserConfigurationException e) {
             		Log.err(e.getMessage());
             	}
diff --git a/beast-pkgmgmt/src/main/java/beast/pkgmgmt/BEASTClassLoader.java b/beast-pkgmgmt/src/main/java/beast/pkgmgmt/BEASTClassLoader.java
index c980753c..37a03720 100644
--- a/beast-pkgmgmt/src/main/java/beast/pkgmgmt/BEASTClassLoader.java
+++ b/beast-pkgmgmt/src/main/java/beast/pkgmgmt/BEASTClassLoader.java
@@ -76,6 +76,14 @@ public static Class<?> forName(String className) throws ClassNotFoundException {
             ClassLoader loader = class2loaderMap.get(className);
             try {
                 return Class.forName(className, false, loader);
+            } catch (ClassNotFoundException e) {
+                // The mapped loader cannot see this class. This happens when the
+                // provider was registered from a version.xml scan (via
+                // resolveLoaderFor → fallback system/context loader) before the
+                // owning package's plugin ModuleLayer was registered: the later
+                // putIfAbsent in registerPluginLayer() then cannot replace the
+                // stale fallback loader. Fall through to search the plugin layers
+                // and correct the mapping below.
             } catch (NoClassDefFoundError e) {
                 String missing = e.getMessage();
                 if (missing != null && (missing.startsWith("beastfx/") || missing.startsWith("beastfx.")
@@ -91,8 +99,15 @@ public static Class<?> forName(String className) throws ClassNotFoundException {
         // 2. Plugin layers (external BEAST packages)
         for (ModuleLayer layer : pluginLayers) {
             for (Module module : layer.modules()) {
+                ClassLoader mcl = module.getClassLoader();
+                if (mcl == null) continue;
                 try {
-                    return Class.forName(className, false, module.getClassLoader());
+                    Class<?> c = Class.forName(className, false, mcl);
+                    // Self-heal: cache the loader that actually resolved the
+                    // class so subsequent lookups skip the failing mapped loader
+                    // (and the exception-driven fall-through above).
+                    class2loaderMap.put(className, mcl);
+                    return c;
                 } catch (ClassNotFoundException | NoClassDefFoundError e) {
                     // try next module
                 }
@@ -559,6 +574,20 @@ private static ClassLoader resolveLoaderFor(String provider) {
                 if (loader != null) return loader;
             }
         }
+        // Also consult already-registered plugin layers: a package's classes
+        // live in its own plugin ModuleLayer (e.g. beast.fx for the BEAUti
+        // input editors), not in the boot layer. Without this, providers listed
+        // in a version.xml would be mapped to the fallback system loader, which
+        // cannot load them, leaving forName() to fall through on every lookup.
+        for (ModuleLayer layer : pluginLayers) {
+            for (Module m : layer.modules()) {
+                java.lang.module.ModuleDescriptor desc = m.getDescriptor();
+                if (desc != null && desc.packages().contains(pkg)) {
+                    ClassLoader loader = m.getClassLoader();
+                    if (loader != null) return loader;
+                }
+            }
+        }
         return fallbackClassLoader();
     }
 }
diff --git a/beast-pkgmgmt/src/test/java/beast/pkgmgmt/ModuleLayerCrossDependencyTest.java b/beast-pkgmgmt/src/test/java/beast/pkgmgmt/ModuleLayerCrossDependencyTest.java
index 8771cdcb..fa2d3449 100644
--- a/beast-pkgmgmt/src/test/java/beast/pkgmgmt/ModuleLayerCrossDependencyTest.java
+++ b/beast-pkgmgmt/src/test/java/beast/pkgmgmt/ModuleLayerCrossDependencyTest.java
@@ -9,12 +9,15 @@
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
+import java.util.Set;
 import java.util.jar.JarEntry;
 import java.util.jar.JarOutputStream;
 import java.util.spi.ToolProvider;
 import java.util.stream.Stream;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 /**
@@ -64,6 +67,47 @@ public void dependentPackageResolvesAgainstAnotherPluginLayer() throws Exception
         assertEquals("base+plugin", result, "cross-layer call should execute");
     }
 
+    /**
+     * Regression test for the BEAUti "ClassNotFoundException: beastfx.app.inputeditor.*"
+     * failure. A package's service providers are listed in its version.xml. If a
+     * version.xml scan registers a provider (via addServices → resolveLoaderFor)
+     * before the owning package's plugin ModuleLayer is registered, the provider
+     * is mapped to the fallback system loader, which cannot load it. registerPluginLayer()
+     * uses putIfAbsent and so cannot replace that stale mapping. forName() must still
+     * resolve the class by falling through to the plugin layers.
+     */
+    @Test
+    public void forNameHealsStaleFallbackLoaderMapping() throws Exception {
+        ToolProvider javac = ToolProvider.findFirst("javac").orElse(null);
+        Assumptions.assumeTrue(javac != null, "no javac tool available - skipping");
+
+        Path work = Files.createTempDirectory("stale-loader-test");
+
+        // A modular jar exporting a provider class, mimicking beast.fx's input editors.
+        Path editorJar = buildModuleJar(javac, work, "fxstaletest", null,
+                "module fxstaletest { exports fxstaletest; }",
+                "fxstaletest", "Editor",
+                "package fxstaletest; public class Editor { }");
+
+        // 1. Simulate the version.xml scan that runs before the plugin layer exists:
+        //    the provider is mapped to the fallback system loader (cannot load it).
+        Map<String, Set<String>> services = Map.of(
+                "fxstaletest.InputEditor", Set.of("fxstaletest.Editor"));
+        BEASTClassLoader.classLoader.addServices("FxStaleTest", services);
+
+        // 2. Register the package's real plugin layer. putIfAbsent leaves the
+        //    stale fallback mapping from step 1 in place.
+        boolean loaded = PackageManager.createAndRegisterModuleLayer(
+                List.of(editorJar), null, "FxStaleTest", "1.0", "FxStaleTest");
+        assertTrue(loaded, "provider module should load into a plugin layer");
+
+        // 3. Despite the stale mapping, forName must resolve the class via the
+        //    plugin layer (previously threw ClassNotFoundException here).
+        Class<?> editor = BEASTClassLoader.forName("fxstaletest.Editor");
+        assertNotNull(editor);
+        assertEquals("fxstaletest.Editor", editor.getName());
+    }
+
     /** Compile a single-package module and pack it into a jar; return the jar path. */
     private static Path buildModuleJar(ToolProvider javac, Path work, String moduleName,
                                        Path modulePathJar, String moduleInfo,
diff --git a/release/Linux/assemble-bundle.sh b/release/Linux/assemble-bundle.sh
index eeb14426..3c0e901e 100755
--- a/release/Linux/assemble-bundle.sh
+++ b/release/Linux/assemble-bundle.sh
@@ -152,21 +152,24 @@ else
     echo "    WARNING: DensiTree.jar not found — densitree script will not work"
 fi
 
-# ── Step 6: Copy examples ─────────────────────────────────────────────────────
+# ── Step 6: Extract examples from the BEAST.base package zip ──────────────────
+# The bundle-root examples/ are extracted from the same package zip seeded into
+# the user dir (lib/packages/), so the example set has a single source of truth
+# (beast-base/src/assembly/package.xml) and the bundle-root and packaged copies
+# cannot drift. The bundle-root copy is kept so `beast -validate examples/...`
+# works from the install dir before first-run seeding.
 echo ""
-echo "==> Step 6: Copying examples..."
-EXAMPLES_DIR="$REPO_ROOT/beast-base/src/test/resources/beast.base/examples"
-if [ -d "$EXAMPLES_DIR" ]; then
-    find "$EXAMPLES_DIR" -maxdepth 1 -name "*.xml" -exec cp {} "$BUNDLE/examples/" \;
-    mkdir -p "$BUNDLE/examples/spec"
-    [ -d "$EXAMPLES_DIR/spec" ] && \
-        find "$EXAMPLES_DIR/spec" -maxdepth 1 -name "*.xml" -exec cp {} "$BUNDLE/examples/spec/" \;
-    [ -d "$EXAMPLES_DIR/nexus" ] && cp -r "$EXAMPLES_DIR/nexus" "$BUNDLE/examples/"
-    EXAMPLE_COUNT=$(find "$BUNDLE/examples" -name "*.xml" | wc -l | tr -d ' ')
-    echo "    Copied ${EXAMPLE_COUNT} example XML files (incl. spec/)"
-else
-    echo "    WARNING: examples not found at $EXAMPLES_DIR"
-fi
+echo "==> Step 6: Extracting examples from $(basename "$BASE_PKG_ZIP")..."
+# Extract the full zip to a temp dir then copy examples/ — avoids unzip glob
+# portability issues where 'examples/*' may not match subdirs on some platforms.
+# Which subdirs are included/excluded is controlled by the include patterns in
+# beast-base/src/assembly/package.xml (e.g. spec/*.xml excludes spec/beast2vs1/).
+EXAMPLES_TMP=$(mktemp -d)
+unzip -o -q "$BASE_PKG_ZIP" -d "$EXAMPLES_TMP"
+cp -r "$EXAMPLES_TMP/examples/." "$BUNDLE/examples/"
+rm -rf "$EXAMPLES_TMP"
+EXAMPLE_COUNT=$(find "$BUNDLE/examples" -name "*.xml" | wc -l | tr -d ' ')
+echo "    Extracted ${EXAMPLE_COUNT} example XML files (incl. spec/)"
 
 # ── Step 7: Copy version.xml and docs ────────────────────────────────────────
 echo ""
diff --git a/release/Linux/linuxbin/applauncher b/release/Linux/linuxbin/applauncher
index 759324fd..3b359171 100755
--- a/release/Linux/linuxbin/applauncher
+++ b/release/Linux/linuxbin/applauncher
@@ -44,11 +44,11 @@ else
 fi
 
 if [ -n "$BEAST_EXTRA_LIBS" ]; then
-  exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+  exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
       -Xss256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -Dfile.encoding=UTF-8 \
       -m beast.pkgmgmt/beast.pkgmgmt.launcher.AppLauncherLauncher "$@"
 else
-  exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+  exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
       -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
       -m beast.pkgmgmt/beast.pkgmgmt.launcher.AppLauncherLauncher "$@"
 fi
diff --git a/release/Linux/linuxbin/beast b/release/Linux/linuxbin/beast
index 16aae175..08fd0885 100755
--- a/release/Linux/linuxbin/beast
+++ b/release/Linux/linuxbin/beast
@@ -69,6 +69,6 @@ if [ -n "$BEAST_EXTRA_LIBS" ]; then
 	fi
 fi
 
-exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Djava.library.path="$LD_LIBRARY_PATH" -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.BeastLauncher "$@"
diff --git a/release/Linux/linuxbin/beauti b/release/Linux/linuxbin/beauti
index 29d61bb8..1efd8a24 100755
--- a/release/Linux/linuxbin/beauti
+++ b/release/Linux/linuxbin/beauti
@@ -25,6 +25,6 @@ JAVA_HOME="$BUNDLE_HOME/jre"
 export JAVA_HOME
 JAVA="$JAVA_HOME/bin/java"
 APP="$BUNDLE_HOME/lib"
-exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.BeautiLauncher -capture "$@"
diff --git a/release/Linux/linuxbin/loganalyser b/release/Linux/linuxbin/loganalyser
index 99c03655..58a9beab 100755
--- a/release/Linux/linuxbin/loganalyser
+++ b/release/Linux/linuxbin/loganalyser
@@ -44,11 +44,11 @@ else
 fi
 
 if [ -n "$BEAST_EXTRA_LIBS" ]; then
-  exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+  exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
       -Xss256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -Dfile.encoding=UTF-8 \
       -m beast.pkgmgmt/beast.pkgmgmt.launcher.AppLauncherLauncher beastfx.app.tools.LogAnalyser "$@"
 else
-  exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+  exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
       -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
       -m beast.pkgmgmt/beast.pkgmgmt.launcher.AppLauncherLauncher beastfx.app.tools.LogAnalyser "$@"
 fi
diff --git a/release/Linux/linuxbin/logcombiner b/release/Linux/linuxbin/logcombiner
index ae1b372e..db047bb5 100755
--- a/release/Linux/linuxbin/logcombiner
+++ b/release/Linux/linuxbin/logcombiner
@@ -25,6 +25,6 @@ JAVA_HOME="$BUNDLE_HOME/jre"
 export JAVA_HOME
 JAVA="$JAVA_HOME/bin/java"
 APP="$BUNDLE_HOME/lib"
-exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.LogCombinerLauncher "$@"
diff --git a/release/Linux/linuxbin/packagemanager b/release/Linux/linuxbin/packagemanager
index c5e5f517..620a6a19 100755
--- a/release/Linux/linuxbin/packagemanager
+++ b/release/Linux/linuxbin/packagemanager
@@ -25,6 +25,6 @@ JAVA_HOME="$BUNDLE_HOME/jre"
 export JAVA_HOME
 JAVA="$JAVA_HOME/bin/java"
 APP="$BUNDLE_HOME/lib"
-exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.PackageManager "$@"
diff --git a/release/Linux/linuxbin/treeannotator b/release/Linux/linuxbin/treeannotator
index df815c5b..f8a16844 100755
--- a/release/Linux/linuxbin/treeannotator
+++ b/release/Linux/linuxbin/treeannotator
@@ -25,6 +25,6 @@ JAVA_HOME="$BUNDLE_HOME/jre"
 export JAVA_HOME
 JAVA="$JAVA_HOME/bin/java"
 APP="$BUNDLE_HOME/lib"
-exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+exec "$JAVA" --module-path "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.TreeAnnotatorLauncher "$@"
diff --git a/release/Mac/build-sign-dmg.sh b/release/Mac/build-sign-dmg.sh
index 633a21ae..812c886e 100755
--- a/release/Mac/build-sign-dmg.sh
+++ b/release/Mac/build-sign-dmg.sh
@@ -226,7 +226,8 @@ sed -i '' 's|^app\.mainclass=.*|app.mainmodule=beast.pkgmgmt/beast.pkgmgmt.launc
 # media) come along automatically.
 sed -i '' '/^\[JavaOptions\]/a\
 java-options=--module-path=\$APPDIR\
-java-options=--add-modules=ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject
+java-options=--add-modules=ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject\
+java-options=--enable-native-access=javafx.graphics,javafx.media,javafx.web
 ' "$BEAST_CFG"
 
 # jpackage may strip bin/java from the bundled runtime (it uses its own native
@@ -295,12 +296,12 @@ build_wrapper_app() {
     local launch_cmd
     if [ -n "$extra_args" ]; then
         launch_cmd="exec \"\$BEAST_APP/runtime/Contents/Home/bin/java\" \\
-    --module-path \"\$BEAST_APP/app\" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \\
+    --module-path \"\$BEAST_APP/app\" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \\
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \\
     -m $module_name/$main_class $extra_args \"\$@\""
     else
         launch_cmd="exec \"\$BEAST_APP/runtime/Contents/Home/bin/java\" \\
-    --module-path \"\$BEAST_APP/app\" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \\
+    --module-path \"\$BEAST_APP/app\" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \\
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \\
     -m $module_name/$main_class \"\$@\""
     fi
@@ -558,21 +559,15 @@ else
 fi
 
 # ── examples/ — example BEAST XML files ──────────────────────────────────────
-EXAMPLES_DIR="$REPO_ROOT/beast-base/src/test/resources/beast.base/examples"
-if [ -d "$EXAMPLES_DIR" ]; then
-    echo "    Copying examples/..."
-    mkdir -p "$OUTPUT/examples"
-    # Copy top-level XML files
-    find "$EXAMPLES_DIR" -maxdepth 1 -name "*.xml" -exec cp {} "$OUTPUT/examples/" \;
-    # Copy nexus subdirectory
-    if [ -d "$EXAMPLES_DIR/nexus" ]; then
-        cp -r "$EXAMPLES_DIR/nexus" "$OUTPUT/examples/nexus"
-    fi
-    if [ -d "$EXAMPLES_DIR/spec" ]; then
-        cp -r "$EXAMPLES_DIR/spec" "$OUTPUT/examples/spec"
-    fi
+# Extracted from the BEAST.base package zip seeded into the user dir
+# (Contents/app/packages/), so the example set has a single source of truth
+# (beast-base/src/assembly/package.xml) and the bundle-root and packaged copies
+# cannot drift. The bundle-root copy is kept so `beast -validate examples/...`
+# works from the install dir before first-run seeding.
+if [ -n "$BASE_PKG_ZIP" ] && unzip -o -q "$BASE_PKG_ZIP" 'examples/*' -d "$OUTPUT"; then
+    echo "    Extracted examples/ from $(basename "$BASE_PKG_ZIP")"
 else
-    echo "    WARNING: $EXAMPLES_DIR not found — skipping examples/"
+    echo "    WARNING: no examples found in BEAST.base package zip — skipping examples/"
 fi
 
 # ── README and LICENSE ─────────────────────────────────────────────────────
diff --git a/release/Mac/macbin/applauncher b/release/Mac/macbin/applauncher
index 2174ef5a..b40201ab 100755
--- a/release/Mac/macbin/applauncher
+++ b/release/Mac/macbin/applauncher
@@ -45,12 +45,12 @@ fi
 
 if [ -n "$BEAST_EXTRA_LIBS" ]; then
   "$JAVA" -Dlauncher.wait.for.exit=true \
-      --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+      --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
       -Xss256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -Dfile.encoding=UTF-8 \
       -m beast.pkgmgmt/beast.pkgmgmt.launcher.AppLauncherLauncher "$@"
 else
   "$JAVA" -Dlauncher.wait.for.exit=true \
-      --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+      --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
       -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
       -m beast.pkgmgmt/beast.pkgmgmt.launcher.AppLauncherLauncher "$@"
 fi
diff --git a/release/Mac/macbin/beast b/release/Mac/macbin/beast
index 44e65502..abe98497 100755
--- a/release/Mac/macbin/beast
+++ b/release/Mac/macbin/beast
@@ -71,6 +71,6 @@ if [ -n "$BEAST_EXTRA_LIBS" ]; then
 fi
 
 "$JAVA" -Dlauncher.wait.for.exit=true \
-    --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+    --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Djava.library.path="$LD_LIBRARY_PATH" -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.BeastLauncher "$@"
diff --git a/release/Mac/macbin/beauti b/release/Mac/macbin/beauti
index d90de718..b5a1c14d 100755
--- a/release/Mac/macbin/beauti
+++ b/release/Mac/macbin/beauti
@@ -27,6 +27,6 @@ BEAST_APP="$BEAST/BEAST.app/Contents"
 export JAVA_HOME="$BEAST_APP/runtime/Contents/Home"
 JAVA="$JAVA_HOME/bin/java"
 "$JAVA" -Dlauncher.wait.for.exit=true \
-    --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+    --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.BeautiLauncher -capture "$@"
diff --git a/release/Mac/macbin/loganalyser b/release/Mac/macbin/loganalyser
index c56529f6..169879a3 100755
--- a/release/Mac/macbin/loganalyser
+++ b/release/Mac/macbin/loganalyser
@@ -45,12 +45,12 @@ fi
 
 if [ -n "$BEAST_EXTRA_LIBS" ]; then
   "$JAVA" -Dlauncher.wait.for.exit=true \
-      --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+      --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
       -Xss256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -Dfile.encoding=UTF-8 \
       -m beast.pkgmgmt/beast.pkgmgmt.launcher.AppLauncherLauncher beastfx.app.tools.LogAnalyser "$@"
 else
   "$JAVA" -Dlauncher.wait.for.exit=true \
-      --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+      --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
       -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
       -m beast.pkgmgmt/beast.pkgmgmt.launcher.AppLauncherLauncher beastfx.app.tools.LogAnalyser "$@"
 fi
diff --git a/release/Mac/macbin/logcombiner b/release/Mac/macbin/logcombiner
index 7064c40e..525e84ac 100755
--- a/release/Mac/macbin/logcombiner
+++ b/release/Mac/macbin/logcombiner
@@ -27,6 +27,6 @@ BEAST_APP="$BEAST/BEAST.app/Contents"
 export JAVA_HOME="$BEAST_APP/runtime/Contents/Home"
 JAVA="$JAVA_HOME/bin/java"
 "$JAVA" -Dlauncher.wait.for.exit=true \
-    --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+    --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.LogCombinerLauncher "$@"
diff --git a/release/Mac/macbin/packagemanager b/release/Mac/macbin/packagemanager
index e097f687..8d1012af 100755
--- a/release/Mac/macbin/packagemanager
+++ b/release/Mac/macbin/packagemanager
@@ -27,6 +27,6 @@ BEAST_APP="$BEAST/BEAST.app/Contents"
 export JAVA_HOME="$BEAST_APP/runtime/Contents/Home"
 JAVA="$JAVA_HOME/bin/java"
 "$JAVA" \
-    --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+    --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.PackageManager "$@"
diff --git a/release/Mac/macbin/treeannotator b/release/Mac/macbin/treeannotator
index 9ce4c93a..87e6b82b 100755
--- a/release/Mac/macbin/treeannotator
+++ b/release/Mac/macbin/treeannotator
@@ -27,6 +27,6 @@ BEAST_APP="$BEAST/BEAST.app/Contents"
 export JAVA_HOME="$BEAST_APP/runtime/Contents/Home"
 JAVA="$JAVA_HOME/bin/java"
 "$JAVA" -Dlauncher.wait.for.exit=true \
-    --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject \
+    --module-path "$BEAST_APP/app" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.TreeAnnotatorLauncher "$@"
diff --git a/release/Windows/assemble-bundle.sh b/release/Windows/assemble-bundle.sh
index 8e4647ab..8d37cee4 100644
--- a/release/Windows/assemble-bundle.sh
+++ b/release/Windows/assemble-bundle.sh
@@ -232,7 +232,7 @@ for cfg in "$BUNDLE/app/"*.cfg; do
     sed -i \
         -e '/^app\.classpath/d' \
         -e 's|^app\.mainclass=\(.*\)|app.mainmodule=beast.pkgmgmt/\1|' \
-        -e '/^\[JavaOptions\]/a java-options=--module-path=$APPDIR\njava-options=--add-modules=ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject' \
+        -e '/^\[JavaOptions\]/a java-options=--module-path=$APPDIR\njava-options=--add-modules=ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject\njava-options=--enable-native-access=javafx.graphics,javafx.media,javafx.web' \
         "$cfg"
 done
 
@@ -244,21 +244,24 @@ WINBIN_DIR="$SCRIPT_DIR/bat"
 mkdir -p "$BUNDLE/bat"
 cp "$WINBIN_DIR/"*.bat "$BUNDLE/bat/"
 
-# ── Step 7: Copy examples ─────────────────────────────────────────────────────
+# ── Step 7: Extract examples from the BEAST.base package zip ──────────────────
+# The bundle-root examples/ are extracted from the same package zip seeded into
+# the user dir (app/packages/), so the example set has a single source of truth
+# (beast-base/src/assembly/package.xml) and the bundle-root and packaged copies
+# cannot drift. The bundle-root copy is kept so `beast -validate examples/...`
+# works from the install dir before first-run seeding.
 echo ""
-echo "==> Step 7: Copying examples..."
-EXAMPLES_DIR="$REPO_ROOT/beast-base/src/test/resources/beast.base/examples"
-if [ -d "$EXAMPLES_DIR" ]; then
-    mkdir -p "$BUNDLE/examples/spec"
-    find "$EXAMPLES_DIR" -maxdepth 1 -name "*.xml" -exec cp {} "$BUNDLE/examples/" \;
-    [ -d "$EXAMPLES_DIR/spec" ] && \
-        find "$EXAMPLES_DIR/spec" -maxdepth 1 -name "*.xml" -exec cp {} "$BUNDLE/examples/spec/" \;
-    [ -d "$EXAMPLES_DIR/nexus" ] && cp -r "$EXAMPLES_DIR/nexus" "$BUNDLE/examples/"
-    EXAMPLE_COUNT=$(find "$BUNDLE/examples" -name "*.xml" | wc -l | tr -d ' ')
-    echo "    Copied ${EXAMPLE_COUNT} example XML files (incl. spec/)"
-else
-    echo "    WARNING: examples not found at $EXAMPLES_DIR"
-fi
+echo "==> Step 7: Extracting examples from $(basename "$BASE_PKG_ZIP")..."
+# Extract the full zip to a temp dir then copy examples/ — avoids unzip glob
+# portability issues where 'examples/*' may not match subdirs on some platforms.
+# Which subdirs are included/excluded is controlled by the include patterns in
+# beast-base/src/assembly/package.xml (e.g. spec/*.xml excludes spec/beast2vs1/).
+EXAMPLES_TMP=$(mktemp -d)
+unzip -o -q "$BASE_PKG_ZIP" -d "$EXAMPLES_TMP"
+cp -r "$EXAMPLES_TMP/examples/." "$BUNDLE/examples/"
+rm -rf "$EXAMPLES_TMP"
+EXAMPLE_COUNT=$(find "$BUNDLE/examples" -name "*.xml" | wc -l | tr -d ' ')
+echo "    Extracted ${EXAMPLE_COUNT} example XML files (incl. spec/)"
 
 # ── Step 8: Copy version.xml and docs ────────────────────────────────────────
 echo ""
diff --git a/release/Windows/bat/applauncher.bat b/release/Windows/bat/applauncher.bat
index 40b6720c..f8e2dc99 100644
--- a/release/Windows/bat/applauncher.bat
+++ b/release/Windows/bat/applauncher.bat
@@ -2,6 +2,6 @@
 set "BUNDLE_HOME=%~dp0.."
 "%BUNDLE_HOME%\runtime\bin\java.exe" ^
     --module-path "%BUNDLE_HOME%\app" ^
-    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject ^
+    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web ^
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 ^
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.AppLauncherLauncher %*
\ No newline at end of file
diff --git a/release/Windows/bat/beast.bat b/release/Windows/bat/beast.bat
index e503399c..fde9b090 100644
--- a/release/Windows/bat/beast.bat
+++ b/release/Windows/bat/beast.bat
@@ -2,6 +2,6 @@
 set "BUNDLE_HOME=%~dp0.."
 "%BUNDLE_HOME%\runtime\bin\java.exe" ^
     --module-path "%BUNDLE_HOME%\app" ^
-    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject ^
+    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web ^
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 ^
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.BeastLauncher %*
diff --git a/release/Windows/bat/beauti.bat b/release/Windows/bat/beauti.bat
index 12b19ac3..0813eae2 100644
--- a/release/Windows/bat/beauti.bat
+++ b/release/Windows/bat/beauti.bat
@@ -2,6 +2,6 @@
 set "BUNDLE_HOME=%~dp0.."
 "%BUNDLE_HOME%\runtime\bin\java.exe" ^
     --module-path "%BUNDLE_HOME%\app" ^
-    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject ^
+    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web ^
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 ^
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.BeautiLauncher -capture %*
\ No newline at end of file
diff --git a/release/Windows/bat/loganalyser.bat b/release/Windows/bat/loganalyser.bat
index 10a447cf..5bb25482 100644
--- a/release/Windows/bat/loganalyser.bat
+++ b/release/Windows/bat/loganalyser.bat
@@ -2,6 +2,6 @@
 set "BUNDLE_HOME=%~dp0.."
 "%BUNDLE_HOME%\runtime\bin\java.exe" ^
     --module-path "%BUNDLE_HOME%\app" ^
-    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject ^
+    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web ^
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 ^
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.AppLauncherLauncher beastfx.app.tools.LogAnalyser %*
\ No newline at end of file
diff --git a/release/Windows/bat/logcombiner.bat b/release/Windows/bat/logcombiner.bat
index a0ab36ed..859f7e57 100644
--- a/release/Windows/bat/logcombiner.bat
+++ b/release/Windows/bat/logcombiner.bat
@@ -2,6 +2,6 @@
 set "BUNDLE_HOME=%~dp0.."
 "%BUNDLE_HOME%\runtime\bin\java.exe" ^
     --module-path "%BUNDLE_HOME%\app" ^
-    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject ^
+    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web ^
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 ^
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.LogCombinerLauncher %*
\ No newline at end of file
diff --git a/release/Windows/bat/packagemanager.bat b/release/Windows/bat/packagemanager.bat
index a2292f39..c3f26e8d 100644
--- a/release/Windows/bat/packagemanager.bat
+++ b/release/Windows/bat/packagemanager.bat
@@ -2,6 +2,6 @@
 set "BUNDLE_HOME=%~dp0.."
 "%BUNDLE_HOME%\runtime\bin\java.exe" ^
     --module-path "%BUNDLE_HOME%\app" ^
-    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject ^
+    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web ^
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 ^
     -m beast.pkgmgmt/beast.pkgmgmt.PackageManager %*
\ No newline at end of file
diff --git a/release/Windows/bat/treeannotator.bat b/release/Windows/bat/treeannotator.bat
index 6b9fe944..449a2140 100644
--- a/release/Windows/bat/treeannotator.bat
+++ b/release/Windows/bat/treeannotator.bat
@@ -2,6 +2,6 @@
 set "BUNDLE_HOME=%~dp0.."
 "%BUNDLE_HOME%\runtime\bin\java.exe" ^
     --module-path "%BUNDLE_HOME%\app" ^
-    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject ^
+    --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web ^
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 ^
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.TreeAnnotatorLauncher %*
\ No newline at end of file