fix beauti clone bug and revive CloneTest #130

[walterxie]

Fixes #130

Summary

Cloning a site model (e.g. HKY, GTR) across partitions in BEAUti inflated the cloned
freqParameter's dimension from N to N² (4 → 16 for nucleotide frequencies), producing an
XML file that BEAST could not run.

Bug location

BeautiDoc.deepCopyPlugin() in beast-fx/src/main/java/beastfx/app/inputeditor/BeautiDoc.java
(~line 2364-2395). When copying a List-valued input, the code iterated once per element
of the source list, but on each iteration called copy.setInputValue(input.getName(), input.get())
— passing the entire source list, not the current element. Input.setValue() appends all
elements of a given list to the destination (Input.java:452-461), so this would over-fill the
copy on every pass.

This was previously masked by a special case: if copy instanceof Parameter.Base, the destination
list was clear()-ed before each setInputValue call, so each pass reset-then-refilled to the
correct size. But Parameter.Base (beast.base.inference.parameter.Parameter.Base) is BEAST3's
now-@Deprecated legacy parameter class. The new spec-based parameters used by BEAUti's
site-model templates — SimplexParam → RealVectorParam → KeyVectorParam → StateNode — no
longer extend it. So copy instanceof Parameter.Base is false for a SimplexParam (e.g.
freqParameter), the clear() never runs, and the whole source list gets appended once per
source element: a dimension-4 list appends 4 times → 16 elements.

The bug was already documented by a disabled regression test:
beast-fx/src/test/java/test/beastfx/app/beauti/CloneTest.java —
@Disabled("SimplexParam validation fails when freqParameter is cloned across partitions (dimension mismatch)").

Fix

Stop iterating per-element for primitive-valued lists (the loop never used the per-element
value o anyway — it always re-set the whole list). Instead, detect once whether the source
list holds primitives (vs. BEASTInterface sub-objects, which still need per-element dedup
handling), clear the destination list a single time, and set it once:

if (input.get() instanceof List) {
    List<?> sourceList = (List<?>) input.get();
    boolean isPrimitiveList = sourceList.isEmpty() || !(sourceList.get(0) instanceof BEASTInterface);
    if (isPrimitiveList) {
        // replace the copy's list wholesale instead of appending per source element
        Object dest = copy.getInput(input.getName()).get();
        if (dest instanceof List) {
            ((List<?>) dest).clear();
        }
        copy.setInputValue(input.getName(), input.get());
    } else {
        for (Object o : sourceList) {
            // ... unchanged BEASTInterface element handling
        }
    }
}

This removes the stale Parameter.Base cast, so it works uniformly for legacy and new-style
parameters, and does the clear-then-set exactly once instead of once per element (also
avoiding the redundant O(n²) work of the old code path).

Changes

• BeautiDoc.deepCopyPlugin(): replace the per-element primitive-value copy (gated on the
  stale Parameter.Base check) with a single wholesale list replace.
• CloneTest.simpleSiteModelCloneTest: re-enable (was @Disabled pending this fix).

[walterxie]

Look OK now:

<stateNode id="birthRate.t:29" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal" value="1.0"/>
<stateNode id="kappa.s:26" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal" value="2.0"/>
<stateNode id="freqParameter.s:26" spec="beast.base.spec.inference.parameter.SimplexParam" dimension="4" domain="UnitInterval">0.25 0.25 0.25 0.25</stateNode>
<stateNode id="freqParameter.s:29" spec="beast.base.spec.inference.parameter.SimplexParam" dimension="4" domain="UnitInterval">0.25 0.25 0.25 0.25</stateNode>
<stateNode id="kappa.s:29" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal" value="2.0"/>
<stateNode id="freqParameter.s:47" spec="beast.base.spec.inference.parameter.SimplexParam" dimension="4" domain="UnitInterval">0.25 0.25 0.25 0.25</stateNode>
<stateNode id="kappa.s:47" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal" value="2.0"/>