Don't output top annotations to .ajava files

annotation-file-utilities/src/test/resources/annotations/tests/classfile/all-annotations.jaif

@@ -34,4 +34,3 @@ annotation @G: @Retention(RUNTIME)
 	boolean[] fieldC
 	int fieldD
 	int fieldE
-

framework/src/main/java/org/checkerframework/common/wholeprograminference/WholeProgramInferenceJavaParserStorage.java

@@ -974,6 +974,12 @@ public void wpiPrepareClassForWriting(
       return;
     }
 
+    // fields
+    for (Map.Entry<String, FieldAnnos> fieldEntry : classAnnos.fields.entrySet()) {
+      fieldEntry.getValue().removePrimaryTopAnnotations();
+    }
+
+    // methods
     for (Map.Entry<String, CallableDeclarationAnnos> methodEntry :
         classAnnos.callableDeclarations.entrySet()) {
       String jvmSignature = methodEntry.getKey();
@@ -1103,7 +1109,7 @@ public void writeResultsToFile(OutputFormat outputFormat, BaseTypeChecker checke
   private void writeAjavaFile(Path outputPath, CompilationUnitAnnos root) {
     try (Writer writer = Files.newBufferedWriter(outputPath, StandardCharsets.UTF_8)) {
 
-      // This commented implementation uses JavaParser's lexical preserving printing, which
+      // This commented one-line implementation uses JavaParser's lexical preserving printing, which
       // writes the file such that its formatting is close to the original source file it was
       // parsed from as possible. It is commented out because the JavaParser feature is very buggy
       // and crashes when adding annotations in certain locations.
@@ -1885,6 +1891,21 @@ public void transferAnnotations() {
       }
     }
 
+    /** Removes the primary annotations in the signature that are the top in their hierarchy. */
+    public void removePrimaryTopAnnotations() {
+      if (returnType != null) {
+        returnType.removePrimaryTopAnnotations();
+      }
+      if (receiverType != null) {
+        receiverType.removePrimaryTopAnnotations();
+      }
+      if (parameterTypes != null) {
+        for (AnnotatedTypeMirror atm : parameterTypes) {
+          atm.removePrimaryTopAnnotations();
+        }
+      }
+    }
+
     @Override
     public String toString() {
       StringJoiner sj =
@@ -2047,6 +2068,13 @@ public void transferAnnotations() {
       declaration.setType(newType);
     }
 
+    /** Removes the top annotations from this. */
+    public void removePrimaryTopAnnotations() {
+      if (type != null) {
+        type.removePrimaryTopAnnotations();
+      }
+    }
+
     @Override
     public String toString() {
       return "FieldAnnos [declaration=" + declaration + ", type=" + type + "]";

framework/src/main/java/org/checkerframework/framework/type/AnnotatedTypeFactory.java

@@ -5606,6 +5606,10 @@ public boolean wpiShouldInferTypesForReceivers() {
    *
    * @param className the class that contains the method, for diagnostics only
    * @param methodAnnos the method or constructor annotations to modify
+   * @see #wpiPrepareMethodForWriting(
+   *     WholeProgramInferenceJavaParserStorage.CallableDeclarationAnnos,
+   *     Collection<WholeProgramInferenceJavaParserStorage.CallableDeclarationAnnos>,
+   *     Collection<WholeProgramInferenceJavaParserStorage.CallableDeclarationAnnos>)
    */
   public void wpiPrepareMethodForWriting(String className, AMethod methodAnnos) {
     // This implementation does nothing.
@@ -5676,6 +5680,11 @@ public void wpiPrepareMethodForWriting(
           false,
           false);
     }
+
+    // Remove top annotations on the method signature after the above runs.
+    // This side effect won't affect any future call to wpiPrepareMethodForWriting, because
+    // methodAnnos is a deep copy of the real inference storage data structure.
+    methodAnnos.removePrimaryTopAnnotations();
   }
 
   /**

framework/src/main/java/org/checkerframework/framework/type/AnnotatedTypeMirror.java

@@ -737,7 +737,7 @@ public boolean removePrimaryAnnotationByClass(Class<? extends Annotation> a) {
    * Remove any primary annotation that is in the same qualifier hierarchy as the parameter.
    *
    * @param a an annotation from the same qualifier hierarchy
-   * @return if an annotation was removed
+   * @return true if an annotation was removed
    */
   public boolean removePrimaryAnnotationInHierarchy(AnnotationMirror a) {
     AnnotationMirror prev = this.getPrimaryAnnotationInHierarchy(a);
@@ -747,6 +747,17 @@ public boolean removePrimaryAnnotationInHierarchy(AnnotationMirror a) {
     return false;
   }
 
+  /**
+   * Remove any annotation that is the top annotation in its qualifier hierarchy.
+   *
+   * @return true if an annotation was removed
+   */
+  public boolean removePrimaryTopAnnotations() {
+    int oldSize = primaryAnnotations.size();
+    primaryAnnotations.removeIf(am -> atypeFactory.isTop(am));
+    return oldSize != primaryAnnotations.size();
+  }
+
   /**
    * Removes multiple primary annotations from the type.
    *