pkl-core: Migrate nullness to JSpecify (#1601)

Replace pkl-core's local nullness annotations with JSpecify annotations.
Enable NullAway checking for pkl-core packages except org.pkl.core.ast
and org.pkl.core.stdlib.

Notable code changes:
- Add a dedicated late-init constructor to VmTyped
- Move VmExceptionBuilder's fallback message derivation from withCause()
to build()
- Split VmException rendering between builder-provided messages and
string-backed messages
- Initialize MessageTransport handlers with default throwing handlers
- Update JSON helper collection types to allow nullable values JSON
arrays and objects can contain JSON null,
so the Java Map/List element types need to model nullable elements
explicitly
- Make public command transform APIs accept nullable transformed values 
   Command transforms can produce null for optional/default handling,
so the BiFunction and options-map element types now model that
explicitly
- Make ExecutorSpiException accept nullable message and cause 
Existing call sites can pass nullable causes from Throwable.getCause()
- Remove JSR-305 semantics from `@LateInit`
   JSpecify does not support the same type-qualifier-nickname pattern,
so `@LateInit` is now documentation plus a NullAway
constructor-initialization exemption

Out of scope:
- NullAway checking of org.pkl.core.ast and org.pkl.core.stdlib
- IntelliJ warnings related to `@LateInit` fields
- Removing the JSR-305 dependency, since concurrency annotations are
still in use

pkl-core/src/generator/java/org/pkl/core/generator/MemberRegistryGenerator.java

@@ -39,6 +39,7 @@ import javax.lang.model.element.Modifier;
 import javax.lang.model.element.PackageElement;
 import javax.lang.model.element.TypeElement;
 import javax.lang.model.type.TypeMirror;
+import org.jspecify.annotations.Nullable;
 
 /**
  * Generates a subclass of {@code org.pkl.core.stdlib.registry.ExternalMemberRegistry} for each
@@ -114,6 +115,7 @@ public final class MemberRegistryGenerator extends AbstractProcessor {
         Comparator.comparing(
                 (TypeElement element) -> {
                   var enclosingElement = element.getEnclosingElement();
+                  assert enclosingElement != null;
                   return enclosingElement.getKind() == ElementKind.PACKAGE
                       ? ""
                       : enclosingElement.getSimpleName().toString();
@@ -155,6 +157,7 @@ public final class MemberRegistryGenerator extends AbstractProcessor {
 
     for (var nodeClass : nodeClasses) {
       var enclosingClass = nodeClass.getEnclosingElement();
+      assert enclosingClass != null;
 
       var pklClassName = getAnnotatedPklName(enclosingClass);
       if (pklClassName == null) {
@@ -226,7 +229,7 @@ public final class MemberRegistryGenerator extends AbstractProcessor {
     writeJavaFile(REGISTRY_PACKAGE_NAME, registryFactoryClass.build());
   }
 
-  private String getAnnotatedPklName(Element element) {
+  private @Nullable String getAnnotatedPklName(Element element) {
     for (var annotation : element.getAnnotationMirrors()) {
       var annotationName = annotation.getAnnotationType().asElement().getSimpleName().toString();
 

pkl-core/src/generator/java/org/pkl/core/generator/package-info.java

@@ -0,0 +1,4 @@
+@NullMarked
+package org.pkl.core.generator;
+
+import org.jspecify.annotations.NullMarked;