Use new (spec) input editors to replace legacy editors

[walterxie]

See #157 and fix #162

Replaces the deprecated ParameterInputEditor with the spec
ScalarInputEditor/VectorInputEditor pair, and removes the now-unused
LegacyStandard.xml template.

• Deregister ParameterInputEditor as an InputEditor service; register
  spec.VectorInputEditor.
• Fix BeautiDoc.scrubAll() resolving SiteModelInputEditor.customConnector
  to the legacy class instead of spec.SiteModelInputEditor; update
  SubstModels.xml/Standard.xml connectors accordingly.
• Remove LegacyStandard.xml.
• Fix spec.ScalarInputEditor:
  • clock-rate check used legacy BranchRateModel.Base instead of spec Base
  • hyperprior "estimate" checkbox reveal checked RealScalarParam instead
    of ScalarDistribution, so it never showed for a prior's own
    hyperparameters (e.g. Gamma's alpha/theta)
• Test coverage: FixedMeanRateTest now asserts the checkbox state itself,
  not just the operator's parameter list; added
  TensorDistributionInputEditorTest for Dirichlet incorrectly displayed in the Prior panel #160 (Dirichlet vs IID offering).

Follow-up not included here: VectorInputEditor has no hyperprior-reveal
branch, and BeautiConfig's hyperprior template still builds legacy
Prior/OneOnX/ScaleOperator objects instead of spec ones.

[walterxie]

Bug 1 #164 — MarkovChainDistribution showing IID in the dropdown: Fixed with a small, dedicated MarkovChainDistributionInputEditor (new class, registered for MarkovChainDistribution.class specifically) that never builds a combo box. TensorDistributionInputEditor/IIDInputEditor stay untouched, and MarkovChainDistribution is not registered as a subtemplate — so its row shows no dropdown at all, and it never appears as an alternative for other vectors either.

Bug 2 #165 — estimate checkbox on Uniform/LogUniform/BoundedReal's lower/upper: Fixed in ScalarInputEditor.java — the checkbox is forced invisible for a ScalarDistribution's "lower"/"upper" inputs.

Bug 3 #166 — CoalescentExtendedBayesianSkyline broken: Fixed with no deprecated classes. TreePriors.xml's indicatorsPrior.alltrees now wires IntSum directly into the spec-package Poisson's param input (mirroring the existing pattern in ClockModels.xml's RRateChangesPrior), instead of the old Prior+legacy-Poisson wrapper. Verified via SimpleTreePriorTest's real BEAUti click-through.