[walterxie]

Fixes #205.

JSONProducer wrote each parameter's domain as an object the first time (domain: {spec: "beast.base.spec.domain.PositiveReal"}) and as "@null" after that. As a result, no BEAST 3 model with spec parameters could be written as JSON and read back.

Changes (JSONProducer.inputToJSON)

• New Domain case: writes the short class name, domain: "PositiveReal", as XMLProducer does (XMLProducer.java:1141).
• Domains a class sets itself are not written. SimplexParam fixes UnitInterval in its constructors, and JSONParser rejects a value for an input that is no longer at its default (Multiple entries for non-list input domain). A domain is skipped when a default-constructed object of the same class already holds it, and it differs from the input's declared default. All other domains are still written explicitly, including domain: "Real".

Tests

New beast.base.parser.JSONProducerTest. All 5 tests fail without the fix.

Test	Checks
domainIsWrittenAsShortName	domain: "PositiveReal" / "Real"; no domain objects, no "@null"
sharedDomainIsWrittenForEveryParameter	two parameters sharing PositiveReal both get it (the second used to be "@null")
roundTripKeepsDomains	write → JSONParser.parseFragment → each parameter has the same domain object
roundTripKeepsIntegerDomain	the same for IntVectorParam / NonNegativeInt
domainFixedByTheClassIsNotWritten	SimplexParam writes no domain and parses back with UnitInterval

Validation

• The full beast-base suite (mvn -pl beast-base test) passes: 513 tests, 0 failures, 3 skipped.
• End to end: the BEAST 3 testUCLNclock model from Convert 12 BEAST2 examples to BEAST3 (batch 2); ship SeqGen examples in beast-fx #204, written with JSONProducer, now passes bin/beast -validate. Before the fix it failed with NoSuchMethodException: …PositiveReal.newInstance().

[alexeid]

Thanks Walter, this fixes #205 cleanly, and the tests cover the cases that matter. I checked that the new tests pass with the fix and fail without it. Two notes for later, not blocking:

1. isDomainFixedByClass default-constructs each class by reflection and treats any exception as "not fixed". That works, but it would quietly misjudge a class whose no-argument constructor fails or has side effects. The underlying oddity is JSONParser rejecting a domain equal to the one the class already set ("Multiple entries for non-list input"); relaxing that in the parser would make this check unnecessary.
2. XMLProducer may have the same SimplexParam issue (writing domain="UnitInterval" for a class that fixes it). Worth checking whether XMLParser accepts that.