Add beagle dependency and fix exec:exec for BEAST runs

Add explicit beagle dependency (optional in beast-base but required by
JPMS module graph). Default exec:exec to beast.base module so BEAST
runs without needing beagle native library. BEAUti available via
-Dbeast.module=beast.fx -Dbeast.main=beastfx.app.beauti.Beauti.

Author: alexeid

pom.xml

@@ -40,7 +40,8 @@
 
         <beast.version>2.8.0-beta1</beast.version>
         <javafx.version>25.0.2</javafx.version>
-        <beast.main>beastfx.app.beauti.Beauti</beast.main>
+        <beast.module>beast.base</beast.module>
+        <beast.main>beast.base.minimal.BeastMain</beast.main>
         <beast.args/>
         <beast.pkg.name>MM</beast.pkg.name>
         <beast.pkg.version>1.3.0</beast.pkg.version>
@@ -59,6 +60,13 @@
             <version>${beast.version}</version>
         </dependency>
 
+        <!-- BEAGLE (optional in beast-base, must be explicit for module path) -->
+        <dependency>
+            <groupId>io.github.compevol</groupId>
+            <artifactId>beagle</artifactId>
+            <version>1.0</version>
+        </dependency>
+
         <!-- GUI (optional at runtime) -->
         <dependency>
             <groupId>io.github.compevol</groupId>
@@ -154,17 +162,17 @@
                 </executions>
             </plugin>
 
-            <!-- Run BEAUti or BEAST with morph-models on module path:
-                 mvn exec:exec
-                 mvn exec:exec -Dbeast.main=beast.base.minimal.BeastMain -Dbeast.args="examples/M3982.xml" -->
+            <!-- Run BEAST or BEAUti with morph-models on module path:
+                 mvn exec:exec -Dbeast.args="examples/M3982.xml"
+                 mvn exec:exec -Dbeast.module=beast.fx -Dbeast.main=beastfx.app.beauti.Beauti -->
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>
                 <version>3.5.0</version>
                 <configuration>
                     <executable>java</executable>
                     <workingDirectory>${project.basedir}</workingDirectory>
-                    <commandlineArgs>--module-path %classpath -DBEAST_PACKAGE_PATH=${project.build.outputDirectory} -m beast.fx/${beast.main} ${beast.args}</commandlineArgs>
+                    <commandlineArgs>--module-path %classpath -DBEAST_PACKAGE_PATH=${project.build.outputDirectory} -m ${beast.module}/${beast.main} ${beast.args}</commandlineArgs>
                 </configuration>
             </plugin>