Load BEAUti templates from the class path, not only module layers

[alexeid]

Problem

BeautiDoc discovers fxtemplates/*.xml only inside resolved module layers:

• processTemplate → loadResourceFromModules scans ModuleLayer.boot() + plugin layers for the main template (Standard.xml).
• getTemplateSources enumerates the merge templates via BEASTClassLoader.listResources, which scans the same layers.

That's correct for the installed launcher and for mvn exec:exec -m beast.fx/…Beauti, where the beast modules are on the module path and resolved. But when BEAUti's dependencies are on the class path — embedded in another tool, or under a test runner where everything loads in the unnamed module — no beast.fx module is resolved, both scans find nothing, and template loading fails with:

java.io.IOException: Cannot find template: fxtemplates/Standard.xml

…even though the template is right there in the beast-fx jar at beast.fx/fxtemplates/Standard.xml.

This came up trying to write a headless BEAUti test for a downstream package (bModelTest), where beast-fx is an ordinary jar dependency on the class path.

Change

A class-path fallback in both discovery paths, in BeautiDoc:

• loadResourceFromModules — after the module scan, try the context class loader's getResourceAsStream on the namespaced name (beast.fx/fxtemplates/Standard.xml), then the bare name. Works on any class loader.
• getTemplateSources — after the module scan, enumerate fxtemplates/*.xml by scanning java.class.path entries (jars via ZipFile, directories by listing), reading each from its resource URL via a new UrlTemplateSource.

Both are additive and last-precedence: in a module-path launch the module scan finds everything first, and these fallbacks contribute only duplicates, which getTemplateSources already drops by file name. The content is always read from the jar (or classes dir) via the resource URL — never copied out to disk.

Scope is contained to BEAUti template discovery (getTemplateSources has a single caller). No change to BEASTClassLoader.

Note: a manifest-only Class-Path jar (used by some launchers for very long class paths) is not followed by the java.class.path scan; in that layout the module-layer scan is expected to have covered it.

Verification

• beast-fx BeautiSimpleTest passes unchanged.
• Downstream (bModelTest, beast-fx on the class path under surefire): before this change, BEAUti startup failed with Cannot find template: fxtemplates/Standard.xml; after it, Standard.xml loads from the beast-fx jar and bModelTest.xml is discovered and merged from the package classes — confirmed in the logs (Loading template from module resource: fxtemplates/Standard.xml, Processing class-path resource …/bmodeltest/fxtemplates/bModelTest.xml).