FQN MRCAPrior to its beast.base.spec.* equivalent#12
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The legacy beast.base.evolution.tree.MRCAPrior is @deprecated; its replacement lives in the spec namespace. Two example XMLs each had one such reference. Verified end-to-end via mvn exec:exec with a 50k temporary chainLength on the StrictClock example (restored to 10M before commit); the other example uses the same FQN substitution. Surfaced by the new deprecated-class-reference scan in beast3-migration's XmlScanner.
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Summary
Two example XMLs reference
beast.base.evolution.tree.MRCAPriordirectly viaspec=. That class is@Deprecatedin beast3; the replacement lives atbeast.base.spec.evolution.tree.MRCAPrior. After this change flc has no remaining references to deprecated classes in any of its XMLs or fxtemplates.The substitution was surfaced by the new deprecated-class-reference pass in CompEvol/beast3-migration, which now cross-references every
spec=and<map>value in tracked XMLs against the global@DeprecatedFQN registry and suggests spec replacements where the same simple name exists under.spec..Test plan
mvn -q compile && mvn -q exec:exec -Dbeast.args="-overwrite examples/Human.H3.81-98-elc-StrictClock.xml"runs end-to-end (verified locally with a temporary 50k chainLength, restored to 10M before commit). The other example uses the same FQN substitution.