diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/Main.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/Main.java
index 1e8346fde..c62e00c51 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/Main.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/Main.java
@@ -69,6 +69,7 @@
 import org.checkerframework.afu.scenelib.type.Type;
 import org.checkerframework.afu.scenelib.util.CommandLineUtils;
 import org.checkerframework.afu.scenelib.util.coll.VivifyingMap;
+import org.checkerframework.checker.signature.qual.BinaryName;
 import org.objectweb.asm.TypePath;
 import org.plumelib.options.Option;
 import org.plumelib.options.OptionGroup;
@@ -306,7 +307,7 @@ private static AScene filteredScene(final AScene scene) {
     final AScene filtered = new AScene();
     filtered.packages.putAll(scene.packages);
     filtered.imports.putAll(scene.imports);
-    for (Map.Entry<String, AClass> entry : scene.classes.entrySet()) {
+    for (Map.Entry<@BinaryName String, AClass> entry : scene.classes.entrySet()) {
       String key = entry.getKey();
       AClass clazz0 = entry.getValue();
       AClass clazz1 = filtered.classes.getVivify(key);
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/Criteria.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/Criteria.java
index 364a79bc4..c36ddceb7 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/Criteria.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/Criteria.java
@@ -13,6 +13,7 @@
 import org.checkerframework.afu.scenelib.io.ASTPath;
 import org.checkerframework.afu.scenelib.io.DebugWriter;
 import org.checkerframework.checker.nullness.qual.Nullable;
+import org.checkerframework.checker.signature.qual.BinaryName;
 import org.checkerframework.checker.signature.qual.ClassGetName;
 import org.objectweb.asm.TypePath;
 
@@ -261,8 +262,8 @@ public ASTPath getASTPath() {
    *
    * @return class name from {@link InClassCriterion}, or null if none present
    */
-  public @Nullable @ClassGetName String getClassName() {
-    String result = null;
+  public @Nullable @BinaryName String getClassName() {
+    @BinaryName String result = null;
     for (Criterion c : criteria.values()) {
       if (c.getKind() == Criterion.Kind.IN_CLASS) {
         if (result == null) {
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/InClassCriterion.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/InClassCriterion.java
index 7fb45633d..19e8a17e7 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/InClassCriterion.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/InClassCriterion.java
@@ -11,7 +11,7 @@
 import javax.lang.model.element.Name;
 import org.checkerframework.afu.annotator.scanner.AnonymousClassScanner;
 import org.checkerframework.afu.annotator.scanner.LocalClassScanner;
-import org.checkerframework.checker.signature.qual.ClassGetName;
+import org.checkerframework.checker.signature.qual.BinaryName;
 
 // If there are dollar signs in a name, then there are two
 // possibilities regarding how the dollar sign got there.
@@ -31,7 +31,7 @@ public final class InClassCriterion implements Criterion {
   static boolean debug = false;
 
   /** The class name. */
-  public final @ClassGetName String className;
+  public final @BinaryName String className;
 
   /** If true, require an exact match. */
   private final boolean exactMatch;
@@ -42,7 +42,7 @@ public final class InClassCriterion implements Criterion {
    * @param className the class name
    * @param exactMatch if true, require an exact match
    */
-  public InClassCriterion(@ClassGetName String className, boolean exactMatch) {
+  public InClassCriterion(@BinaryName String className, boolean exactMatch) {
     this.className = className;
     this.exactMatch = exactMatch;
   }
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/Insertions.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/Insertions.java
index 7708df7a9..5ced93159 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/Insertions.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/find/Insertions.java
@@ -46,6 +46,7 @@
 import org.checkerframework.afu.scenelib.type.BoundedType;
 import org.checkerframework.afu.scenelib.type.DeclaredType;
 import org.checkerframework.afu.scenelib.type.Type;
+import org.checkerframework.checker.signature.qual.BinaryName;
 import org.objectweb.asm.TypePath;
 
 /**
@@ -85,7 +86,7 @@ public Insertions() {
    * @return {@link java.util.Set} of {@link Insertion}s with an {@link InClassCriterion} for the
    *     given class
    */
-  public Set<Insertion> forClass(CompilationUnitTree cut, String qualifiedClassName) {
+  public Set<Insertion> forClass(CompilationUnitTree cut, @BinaryName String qualifiedClassName) {
     Set<Insertion> set = new LinkedHashSet<>();
     forClass(cut, qualifiedClassName, set);
     return set;
@@ -110,7 +111,8 @@ public Set<Insertion> forOuterClass(CompilationUnitTree cut, String qualifiedOut
       }
       Set<Insertion> set = new LinkedHashSet<>();
       for (String innerClassPath : map.keySet()) {
-        String qualifiedClassName = qualifiedOuterClassName + innerClassPath;
+        @SuppressWarnings("signature:assignment") // string concatenation
+        @BinaryName String qualifiedClassName = qualifiedOuterClassName + innerClassPath;
         forClass(cut, qualifiedClassName, set);
       }
       return set;
@@ -118,7 +120,8 @@ public Set<Insertion> forOuterClass(CompilationUnitTree cut, String qualifiedOut
   }
 
   /** Side-effects {@code result} to add {@link Insertion}s for {@code qualifiedClassName}. */
-  private void forClass(CompilationUnitTree cut, String qualifiedClassName, Set<Insertion> result) {
+  private void forClass(
+      CompilationUnitTree cut, @BinaryName String qualifiedClassName, Set<Insertion> result) {
     if (Main.temporaryDebug) {
       System.out.printf(
           "calling forClass(cut, %s, set of size %d)%n", qualifiedClassName, result.size());
@@ -243,7 +246,7 @@ public List<Insertion> toList() {
    */
   @SuppressWarnings("CatchAndPrintStackTrace") // maybe rethrow the exception
   private Set<Insertion> organizeTypedInsertions(
-      CompilationUnitTree cut, String className, Collection<Insertion> insertions) {
+      CompilationUnitTree cut, @BinaryName String className, Collection<Insertion> insertions) {
     Map<ASTRecord, TypedInsertion> outerInsertions = new HashMap<>();
     Set<Insertion> innerInsertions = new LinkedHashSet<>();
     List<Insertion> innerInsertionsList = new ArrayList<>();
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/specification/IndexFileSpecification.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/specification/IndexFileSpecification.java
index 2cac6be03..2174df97b 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/specification/IndexFileSpecification.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/annotator/specification/IndexFileSpecification.java
@@ -44,6 +44,7 @@
 import org.checkerframework.afu.scenelib.type.DeclaredType;
 import org.checkerframework.afu.scenelib.type.Type;
 import org.checkerframework.afu.scenelib.util.coll.VivifyingMap;
+import org.checkerframework.checker.signature.qual.BinaryName;
 import org.checkerframework.checker.signature.qual.ClassGetName;
 import org.objectweb.asm.ClassReader;
 import org.objectweb.asm.ClassWriter;
@@ -169,9 +170,8 @@ private void parseScene() {
       parsePackage(clist, entry.getKey(), entry.getValue());
     }
 
-    @SuppressWarnings("signature:assignment") // scene-lib is not fully annotated
-    VivifyingMap<@ClassGetName String, AClass> classes = scene.classes;
-    for (Map.Entry<@ClassGetName String, AClass> entry : classes.entrySet()) {
+    VivifyingMap<@BinaryName String, AClass> classes = scene.classes;
+    for (Map.Entry<@BinaryName String, AClass> entry : classes.entrySet()) {
       String key = entry.getKey();
       AClass clazz = entry.getValue();
       if (key.endsWith(".package-info")) {
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AClass.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AClass.java
index ccf24f330..ec06e0118 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AClass.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AClass.java
@@ -12,6 +12,8 @@
 import javax.lang.model.element.VariableElement;
 import org.checkerframework.afu.scenelib.Annotation;
 import org.checkerframework.afu.scenelib.util.coll.VivifyingMap;
+import org.checkerframework.checker.nullness.qual.MonotonicNonNull;
+import org.checkerframework.checker.nullness.qual.Nullable;
 import org.plumelib.util.CollectionsPlume;
 
 /** An annotated class. */
@@ -45,7 +47,7 @@ public class AClass extends ADeclaration {
    * The type element representing the class. Clients must call {@link #setTypeElement(TypeElement)}
    * before accessing this field.
    */
-  private /*@MonotonicNonNull*/ TypeElement typeElement = null;
+  private @MonotonicNonNull TypeElement typeElement = null;
 
   /** The fully-qualified name of the annotated class. */
   public final String className;
@@ -54,7 +56,7 @@ public class AClass extends ADeclaration {
   private final HashSet<String> enums = new HashSet<>();
 
   /** The enum constants of this class, or null if this class is not an enum. */
-  private /*@MonotonicNonNull*/ List<VariableElement> enumConstants = null;
+  private @MonotonicNonNull List<VariableElement> enumConstants = null;
 
   /**
    * The simple class names any of this class's outer classes (or this class) that are annotations.
@@ -290,7 +292,7 @@ public void markAsEnum(String className) {
    *
    * @return the enum constants, or null if this is not an enum
    */
-  public /*@Nullable*/ List<VariableElement> getEnumConstants() {
+  public @Nullable List<VariableElement> getEnumConstants() {
     if (enumConstants == null) {
       return null;
     }
@@ -409,7 +411,7 @@ public void markAsRecord(String className) {
    *
    * @return a type element representing this class
    */
-  public /*@Nullable*/ TypeElement getTypeElement() {
+  public @Nullable TypeElement getTypeElement() {
     return typeElement;
   }
 
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AMethod.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AMethod.java
index 5156877d7..27016ba08 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AMethod.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AMethod.java
@@ -13,6 +13,7 @@
 import javax.lang.model.type.TypeMirror;
 import org.checkerframework.afu.scenelib.Annotation;
 import org.checkerframework.afu.scenelib.util.coll.VivifyingMap;
+import org.checkerframework.checker.nullness.qual.Nullable;
 
 /** An annotated method; contains bounds, return, parameters, receiver, and throws. */
 public class AMethod extends ADeclaration {
@@ -23,14 +24,14 @@ public class AMethod extends ADeclaration {
   public final String methodSignature;
 
   /** The type parameters of this method. */
-  private /*@Nullable*/ List<? extends TypeParameterElement> typeParameters = null;
+  private @Nullable List<? extends TypeParameterElement> typeParameters = null;
 
   /** The method's annotated type parameter bounds. */
   public final VivifyingMap<BoundLocation, ATypeElement> bounds =
       ATypeElement.<BoundLocation>newVivifyingLHMap_ATE();
 
   /** The return type of the method, or null if the method's return type is unknown or void. */
-  private /*@Nullable*/ TypeMirror returnTypeMirror;
+  private @Nullable TypeMirror returnTypeMirror;
 
   /** The method's annotated return type. Non-null even if returnTypeMirror is null. */
   public final ATypeElement returnType; // initialized in constructor
@@ -230,7 +231,7 @@ public AField vivifyAndAddTypeMirrorToPostcondition(String expression, TypeMirro
    *
    * @return the return type, or null if the return type is unknown or void
    */
-  public /*@Nullable*/ TypeMirror getReturnTypeMirror() {
+  public @Nullable TypeMirror getReturnTypeMirror() {
     return returnTypeMirror;
   }
 
@@ -239,7 +240,7 @@ public AField vivifyAndAddTypeMirrorToPostcondition(String expression, TypeMirro
    *
    * @param returnTypeMirror the return type
    */
-  public void setReturnTypeMirror(/*@Nullable*/ TypeMirror returnTypeMirror) {
+  public void setReturnTypeMirror(@Nullable TypeMirror returnTypeMirror) {
     if (returnTypeMirror == null) {
       return;
     }
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AScene.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AScene.java
index d75d330fd..21eb140aa 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AScene.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/AScene.java
@@ -8,6 +8,8 @@
 import org.checkerframework.afu.scenelib.Annotation;
 import org.checkerframework.afu.scenelib.io.IndexFileParser;
 import org.checkerframework.afu.scenelib.util.coll.VivifyingMap;
+import org.checkerframework.checker.signature.qual.BinaryName;
+import org.checkerframework.checker.signature.qual.ClassGetName;
 
 /**
  * An <code>AScene</code> (annotated scene) represents the annotations on a set of Java classes and
@@ -57,8 +59,8 @@ public class AScene implements Cloneable {
   public final Map<String, Set<String>> imports = new LinkedHashMap<>();
 
   /** This scene's annotated classes; map key is class name */
-  public final VivifyingMap</*@BinaryName*/ String, AClass> classes =
-      new VivifyingMap<String, AClass>(new LinkedHashMap<>()) {
+  public final VivifyingMap<@BinaryName String, AClass> classes =
+      new VivifyingMap<@BinaryName String, AClass>(new LinkedHashMap<>()) {
         @Override
         public AClass createValueFor(String k) {
           return new AClass(k);
@@ -133,7 +135,7 @@ public int hashCode() {
    *
    * @return an immutable map from binary names to AClass objects
    */
-  public Map</*@BinaryName*/ String, AClass> getClasses() {
+  public Map<@ClassGetName String, AClass> getClasses() {
     return ImmutableMap.copyOf(classes);
   }
 
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/LocalLocation.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/LocalLocation.java
index 3610365d3..7e30ce711 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/LocalLocation.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/el/LocalLocation.java
@@ -173,7 +173,7 @@ public boolean equals(LocalLocation o) {
   }
 
   @Override
-  public boolean equals(/*@ReadOnly*/ Object o) {
+  public boolean equals(Object o) {
     return o instanceof LocalLocation && equals((LocalLocation) o);
   }
 
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/ASTIndex.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/ASTIndex.java
index fe50c19a4..fdd107aa1 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/ASTIndex.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/ASTIndex.java
@@ -63,6 +63,7 @@
 import org.checkerframework.afu.annotator.find.CaseUtils;
 import org.checkerframework.afu.scenelib.util.JVMNames;
 import org.checkerframework.afu.scenelib.util.coll.WrapperMap;
+import org.checkerframework.checker.signature.qual.BinaryName;
 
 /** Cache of {@code ASTPath} data for the nodes of a compilation unit tree. */
 public class ASTIndex extends WrapperMap<Tree, ASTRecord> {
@@ -134,7 +135,7 @@ private void saveAll(
            * @param node the class
            */
           private void saveClass(ClassTree node) {
-            String className = ((JCTree.JCClassDecl) node).sym.flatname.toString();
+            @BinaryName String className = ((JCTree.JCClassDecl) node).sym.flatname.toString();
             ASTRecord rec = new ASTRecord(cut, className, null, null, ASTPath.empty());
             counters.push(0);
             node.accept(this, rec);
@@ -261,7 +262,7 @@ public Void visitClass(ClassTree node, ASTRecord rec) {
               if (member.getKind() == Tree.Kind.BLOCK) {
                 save(member, rec, kind, ASTPath.INITIALIZER, i++);
               } else if (ASTPath.isClassEquiv(member.getKind())) {
-                String className = ((JCTree.JCClassDecl) member).sym.flatname.toString();
+                @BinaryName String className = ((JCTree.JCClassDecl) member).sym.flatname.toString();
                 member.accept(this, new ASTRecord(cut, className, null, null, ASTPath.empty()));
               } else {
                 member.accept(this, rec);
@@ -402,7 +403,7 @@ public Void visitNewClass(NewClassTree node, ASTRecord rec) {
             saveAll(node.getArguments(), rec, kind, ASTPath.ARGUMENT);
             if (classBody != null) {
               Name name = classBody.getSimpleName();
-              String className = null;
+              @BinaryName String className = null;
               if (name == null || name.toString().isEmpty()) {
                 int i = counters.pop();
                 counters.push(++i);
@@ -617,7 +618,7 @@ public static Tree getNode(CompilationUnitTree cut, ASTRecord rec) {
     ExpressionTree et = cut.getPackageName();
     String pkg = et == null ? "" : et.toString();
     if (!pkg.isEmpty() && rec.className.indexOf('.') < 0) {
-      String className = pkg + "." + rec.className;
+      @BinaryName String className = pkg + "." + rec.className;
       rec = new ASTRecord(cut, className, rec.methodName, rec.varName, rec.astPath);
     }
     return revIndex.get(rec);
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/ASTRecord.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/ASTRecord.java
index ff11e31fa..59f65da08 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/ASTRecord.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/ASTRecord.java
@@ -10,6 +10,7 @@
 import java.util.ArrayDeque;
 import java.util.Deque;
 import java.util.Objects;
+import org.checkerframework.checker.signature.qual.BinaryName;
 
 /**
  * Structure bundling an {@link ASTPath} with information about its starting point. Necessary
@@ -20,7 +21,7 @@ public class ASTRecord implements Comparable<ASTRecord> {
   public final CompilationUnitTree ast;
 
   /** Name of the enclosing class declaration. */
-  public final String className;
+  public final @BinaryName String className;
 
   /** Name of the enclosing method declaration, or null if there is none. */
   public final String methodName;
@@ -42,7 +43,7 @@ public class ASTRecord implements Comparable<ASTRecord> {
    */
   public ASTRecord(
       CompilationUnitTree ast,
-      String className,
+      @BinaryName String className,
       String methodName,
       String varName,
       ASTPath astPath) {
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/IndexFileParser.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/IndexFileParser.java
index c8ba04948..0450e168e 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/IndexFileParser.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/IndexFileParser.java
@@ -1654,7 +1654,7 @@ private BoundedType parseBoundedType(DeclaredType type) throws IOException, Pars
   private void parseClass() throws IOException, ParseException {
     expectKeyword("class");
     String basename = expectIdentifier();
-    String fullName = curPkgPrefix + basename;
+    @BinaryName String fullName = curPkgPrefix + basename;
 
     AClass c = scene.classes.getVivify(fullName);
     expectChar(':');
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/JavapParser.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/JavapParser.java
index 59db2a7f8..b21ce069d 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/JavapParser.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/JavapParser.java
@@ -392,7 +392,7 @@ private void parse() throws IOException, ParseException {
         trim("class ");
         trim("interface ");
         int nameEnd = line.indexOf(' ');
-        String className = (nameEnd == -1) ? line : line.substring(0, line.indexOf(' '));
+        @BinaryName String className = (nameEnd == -1) ? line : line.substring(0, line.indexOf(' '));
         String pp = IOUtils.packagePart(className);
         String bp = IOUtils.basenamePart(className);
         nextLine();
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/classfile/ClassAnnotationSceneReader.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/classfile/ClassAnnotationSceneReader.java
index 5719cf7e0..ea3d55d8c 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/classfile/ClassAnnotationSceneReader.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/classfile/ClassAnnotationSceneReader.java
@@ -36,6 +36,7 @@
 import org.checkerframework.checker.nullness.qual.Nullable;
 import org.checkerframework.checker.signature.qual.BinaryName;
 import org.checkerframework.checker.signature.qual.ClassGetName;
+import org.checkerframework.checker.signature.qual.InternalForm;
 import org.objectweb.asm.AnnotationVisitor;
 import org.objectweb.asm.ClassReader;
 import org.objectweb.asm.ClassWriter;
@@ -130,10 +131,10 @@ public ClassAnnotationSceneReader(
   public void visit(
       int version,
       int access,
-      String name,
+      @InternalForm String name,
       String signature,
       String superName,
-      String[] interfaces) {
+      @InternalForm String @Nullable [] interfaces) {
     classWriter.visit(version, access, name, signature, superName, interfaces);
     aClass = scene.classes.getVivify(name.replace('/', '.'));
   }
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/classfile/ClassAnnotationSceneWriter.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/classfile/ClassAnnotationSceneWriter.java
index 6cb126a98..427132c7b 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/classfile/ClassAnnotationSceneWriter.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/io/classfile/ClassAnnotationSceneWriter.java
@@ -151,11 +151,12 @@ public byte[] toByteArray() {
     return ((ClassWriter) cv).toByteArray();
   }
 
+  @SuppressWarnings("override.param") // ASM is not annotated
   @Override
   public void visit(
       int version,
       int access,
-      String name,
+      @ClassGetName String name,
       String signature,
       String superName,
       String[] interfaces) {
diff --git a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/tools/IndexFileMerger.java b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/tools/IndexFileMerger.java
index 85fc159f5..2486bb124 100644
--- a/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/tools/IndexFileMerger.java
+++ b/annotation-file-utilities/src/main/java/org/checkerframework/afu/scenelib/tools/IndexFileMerger.java
@@ -32,6 +32,7 @@
 import org.checkerframework.afu.scenelib.io.IndexFileParser;
 import org.checkerframework.afu.scenelib.io.IndexFileWriter;
 import org.checkerframework.afu.scenelib.util.CommandLineUtils;
+import org.checkerframework.checker.signature.qual.BinaryName;
 import org.plumelib.util.FileIOException;
 
 /** Utility for merging index files, including multiple versions for the same class. */
@@ -42,7 +43,7 @@ public static void main(String[] args) {
       System.exit(0);
     }
 
-    final SetMultimap<String, String> annotatedFor = HashMultimap.create();
+    final SetMultimap<@BinaryName String, String> annotatedFor = HashMultimap.create();
     String[] inputArgs;
 
     // TODO: document assumptions
@@ -84,7 +85,8 @@ public static void main(String[] args) {
           int ix = relPath.indexOf(File.separator);
           String subdir = ix < 0 ? relPath : relPath.substring(0, ix);
           // trim .jaif or .jann and subdir, convert directory to package id
-          String classname =
+          @SuppressWarnings("signature:assignment") // string manipulation
+          @BinaryName String classname =
               relPath
                   .substring(0, relPath.lastIndexOf('.'))
                   .substring(relPath.indexOf('/') + 1)
@@ -259,8 +261,9 @@ public Void visitElement(AElement el, Void v) {
       AnnotationDef afDef =
           Annotations.createValueAnnotationDef(
               "AnnotatedFor", Collections.<Annotation>emptySet(), stringArray, "IndexFileMerger");
-      for (Map.Entry<String, Collection<String>> entry : annotatedFor.asMap().entrySet()) {
-        String key = entry.getKey();
+      for (Map.Entry<@BinaryName String, Collection<String>> entry :
+          annotatedFor.asMap().entrySet()) {
+        @BinaryName String key = entry.getKey();
         Collection<String> values = entry.getValue();
         Annotation afAnno =
             new Annotation(