Add missing @Deprecated annotations on three legacy classes#76
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Three classes have spec replacements (or, for PriorInputEditor, an already-deprecated wrapper) but were missing the @deprecated annotation: * BactrianIntervalOperator — already had a @deprecated Javadoc pointing at beast.base.spec.inference.operator.uniform.IntervalOperator, but no annotation. The annotation is what tooling reads. * BranchRateModel.Base — the legacy abstract base. Spec replacement at beast.base.spec.evolution.branchratemodel.Base. * PriorInputEditor — BEAUti editor for the already-deprecated Prior wrapper; no longer needed under the spec framework where distributions take a param input directly. Found via the beast3-migration analyzer, which uses @deprecated as the ground truth for "this class has been replaced". Without these annotations the analyzer (and IDEs) can't warn downstream packages that they're extending a class slated for removal.
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Summary
Three classes have spec replacements (or in the
PriorInputEditorcase, are tied to an already-deprecated wrapper) but are missing the@Deprecatedannotation:BactrianIntervalOperator— already has a@deprecatedJavadoc pointing atbeast.base.spec.inference.operator.uniform.IntervalOperator, but no annotation. Tooling and IDE warnings rely on the annotation, not the Javadoc tag.BranchRateModel.Base— the legacy abstract base. Spec replacement atbeast.base.spec.evolution.branchratemodel.Base.PriorInputEditor— BEAUti editor for the already-deprecatedPriorwrapper. Not needed under the spec framework where distributions take aparaminput directly.Each gains a Javadoc
@deprecatedpointer to the spec replacement (where one exists) and the@Deprecatedannotation itself. Twelve added lines, no logic changes.Why it matters
Found via the beast3-migration analyzer, which uses
@Deprecatedas the canonical signal for "this class has been replaced." Without these annotations the analyzer can't warn downstream packages (BEASTLabs, sampled-ancestors, flc, …) that they're extending a class slated for removal, and IDEs can't show the strikethrough on usages.Test plan
mvn -q -DskipTests compile— cleanmvn -q -DskipTests test-compile— clean