Sync b3xml branch to the latest master branch

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>

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());
             	}

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>

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());
             	}

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();
     }
 }

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,

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 ""

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

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="$LD_LIBRARY_PATH" -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.BeastLauncher "$@"

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 "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.BeautiLauncher -capture "$@"

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

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 "$APP" --add-modules ALL-MODULE-PATH,javafx.controls,javafx.fxml,javafx.swing,javafx.web,jdk.jsobject --enable-native-access=javafx.graphics,javafx.media,javafx.web \
     -Xss256m -Xmx8g -Duser.language=en -Dfile.encoding=UTF-8 \
     -m beast.pkgmgmt/beast.pkgmgmt.launcher.LogCombinerLauncher "$@"