BEAUti template issue

[walterxie]

Two issues:

1. In developer env BEAUti File ▸ Template menu is empty #110 is solved, but after release, it does not work in the user env.

To replicate in the user env, mvn clean package, and then go to release/Mac, and clean folder rm -rf dmg-staging if it exists and run ./build-sign-dmg.sh to create the Mac release for testing. Then go to release/Mac/dmg-staging/BEAST 2.8.0, run ./bin/beauti to replicate the err:

---

2. Install BEASTLab, and choose its new template SelfTuningMCMC from BEAUti, and then it will crash with the following err, and then BEAUti cannot be launched anymore.

mergewith
java.lang.ClassNotFoundException: Could not find class beast.base.core.BEASTInterface as service beast.base.core.BEASTInterface
Perhaps the package is missing or the package is not correctly configured by the developer 
or there is an element without spec attribute
(Developer: check by running beastfx.app.tools.PackageHealthChecker on the package)
	at beast.pkgmgmt@2.8.0-SNAPSHOT/beast.pkgmgmt.BEASTClassLoader.forName(BEASTClassLoader.java:140)
	at beast.base@2.8.0-SNAPSHOT/beast.base.parser.XMLParser.createObject(XMLParser.java:934)
	at beast.base@2.8.0-SNAPSHOT/beast.base.parser.XMLParser.parseTemplate(XMLParser.java:504)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.BeautiDoc.loadTemplate(BeautiDoc.java:1147)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.BeautiDoc.newAnalysis(BeautiDoc.java:408)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.BeautiDoc.loadNewTemplate(BeautiDoc.java:427)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.beauti.BeautiTabPane$TemplateAction.actionPerformed(BeautiTabPane.java:999)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.MyAction.lambda$init$0(MyAction.java:90)
	at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at javafx.base/javafx.event.Event.fireEvent(Unknown Source)
	at javafx.controls/javafx.scene.control.MenuItem.fire(Unknown Source)
	at javafx.controls/com.sun.javafx.scene.control.GlobalMenuAdapter.lambda$bindMenuItemProperties$2(Unknown Source)
	at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at javafx.base/javafx.event.Event.fireEvent(Unknown Source)
	at javafx.controls/javafx.scene.control.MenuItem.fire(Unknown Source)
	at javafx.graphics/com.sun.javafx.tk.quantum.GlassSystemMenu$1.action(Unknown Source)
beast.base.parser.XMLParserException: 
Error 1107 parsing the xml input file

validate and intialize error: Could not find class beast.base.core.BEASTInterface as service beast.base.core.BEASTInterface
Perhaps the package is missing or the package is not correctly configured by the developer 
or there is an element without spec attribute
(Developer: check by running beastfx.app.tools.PackageHealthChecker on the package)

Error detected about here:
  <beast>
      <mergewith>

	at beast.base@2.8.0-SNAPSHOT/beast.base.parser.XMLParser.createObject(XMLParser.java:942)
	at beast.base@2.8.0-SNAPSHOT/beast.base.parser.XMLParser.parseTemplate(XMLParser.java:504)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.BeautiDoc.loadTemplate(BeautiDoc.java:1147)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.BeautiDoc.newAnalysis(BeautiDoc.java:408)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.BeautiDoc.loadNewTemplate(BeautiDoc.java:427)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.beauti.BeautiTabPane$TemplateAction.actionPerformed(BeautiTabPane.java:999)
	at beast.fx@2.8.0-SNAPSHOT/beastfx.app.inputeditor.MyAction.lambda$init$0(MyAction.java:90)
	at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at javafx.base/javafx.event.Event.fireEvent(Unknown Source)
	at javafx.controls/javafx.scene.control.MenuItem.fire(Unknown Source)
	at javafx.controls/com.sun.javafx.scene.control.GlobalMenuAdapter.lambda$bindMenuItemProperties$2(Unknown Source)
	at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at javafx.base/javafx.event.Event.fireEvent(Unknown Source)
	at javafx.controls/javafx.scene.control.MenuItem.fire(Unknown Source)
	at javafx.graphics/com.sun.javafx.tk.quantum.GlassSystemMenu$1.action(Unknown Source)
Jun 24, 2026 2:41:02 PM javafx.scene.control.Menu$6 onChanged
WARNING: Adding MenuItem Other Template that has already been added to Template

[alexeid]

Found it. The template-discovery fix from #110/#111 is correct — it just never reached the running app in the installed build.

Root cause: the release ships BEAST.base/BEAST.app as package zips that BeastLauncher.seedBundledPackage() extracts into the user package dir (~/Library/Application Support/BEAST/2.8/) and loads as plugin module layers. That method only re-extracted when the bundled version was strictly newer than the copy already seeded. The package version string (version.xml) stays 2.8.0 for the whole release cycle, so after mvn clean package + a fresh app build the stale lib/ was kept and the app kept loading the pre-fix beast.fx — hence the empty Template menu. (The crash trace in point 2 above also matches pre-fix line numbers, confirming stale classes were running.)

I verified the discovery code itself works in the release's plugin-layer setup: with a freshly built beast.fx loaded as a plugin layer, BeautiDoc.getAvailableTemplates() returns Standard + LegacyStandard as expected.

Fix (#113): when the user copy reports the same version, seedBundledPackage() now compares a SHA-256 of the bundled zip against a marker written at seed time and re-extracts on mismatch. Strictly newer user copies are never downgraded. This catches development rebuilds and re-released betas, not just SNAPSHOTs.

To re-test on your side once #113 is in: mvn clean package, rebuild the DMG, and launch — the stale package will be replaced automatically. (If you want a clean baseline first, delete ~/Library/Application Support/BEAST/2.8/BEAST.app and .../BEAST.base.)

Point 2 (BEASTLab SelfTuningMCMC): that trace came from the same stale build, so please retest it after #113. The BEASTInterface-as-service / <mergewith> failure may have been a mismatch between BEASTLab and the stale core packages. If it still reproduces on a fresh build, let's track it as a separate issue.