Fix #129: Implement Arrays Validation Rule 20116 for SBaseRef missing indices

[dyrpsf]

Overview

This PR resolves Issue #129, where the Arrays validation was failing to check rule 20116. Previously, if an SBaseRef pointed to an array (an object with a ListOfDimensions) but lacked the required Index objects, the validator would silently pass instead of throwing the expected error.

Changes

• New Validation Rule: Created SBaseRefIndicesCheck.java in the arrays constraints package. This class safely looks up the referenced element (using getIdRef() or getElementByMetaId()) and checks if the target has dimensions. If it does, it verifies that the referencing SBaseRef contains a ListOfIndices.
• Registered Rule 20116: Added ARRAYS_20116 to the GENERAL_CONSISTENCY checklist in ArraysSBasePluginConstraints.java so the JSBML validation engine actively runs the new check.

Validation

• Successfully compiled the arrays extension (mvn clean test-compile -pl extensions/arrays).
• Verified that the changes pass the local test suite (mvn test -pl extensions/arrays).

Closes #129