diff --git a/.ci-build-without-test.sh b/.ci-build-without-test.sh
index 825ad389..3aa0f97f 100755
--- a/.ci-build-without-test.sh
+++ b/.ci-build-without-test.sh
@@ -13,18 +13,31 @@ else
   export JAVA_HOME=${JAVA_HOME:-$(dirname $(dirname $(readlink -f $(which javac))))}
 fi
 
-export JSR308="${JSR308:-$(cd .. && pwd -P)}"
-export AFU="${AFU:-$(pwd -P)/../annotation-tools/annotation-file-utilities}"
-export CHECKERFRAMEWORK="${CHECKERFRAMEWORK:-$(pwd -P)/../checker-framework}"
-
-export PATH=$AFU/scripts:$JAVA_HOME/bin:$PATH
-
 if [ -d "/tmp/plume-scripts" ] ; then
   git -C /tmp/plume-scripts pull -q
 else
   git -C /tmp clone --depth 1 -q https://github.com/plume-lib/plume-scripts.git
 fi
 
+export AFU="${AFU:-../annotation-tools/annotation-file-utilities}"
+# Don't use `AT=${AFU}/..` which causes a git failure.
+AT=$(dirname "${AFU}")
+
+## Build annotation-tools (Annotation File Utilities)
+/tmp/plume-scripts/git-clone-related opprop annotation-tools "${AT}"
+if [ ! -d ../annotation-tools ] ; then
+ ln -s "${AT}" ../annotation-tools
+fi
+
+echo "Running:  (cd ${AT} && ./.build-without-test.sh)"
+(cd "${AT}" && ./.build-without-test.sh)
+echo "... done: (cd ${AT} && ./.build-without-test.sh)"
+
+export JSR308="${JSR308:-$(cd .. && pwd -P)}"
+export CHECKERFRAMEWORK="${CHECKERFRAMEWORK:-$(pwd -P)/../checker-framework}"
+
+export PATH=$AFU/scripts:$JAVA_HOME/bin:$PATH
+
 ## Build Checker Framework
 /tmp/plume-scripts/git-clone-related opprop checker-framework ${CHECKERFRAMEWORK}
 
diff --git a/build.gradle b/build.gradle
index f2049ca1..075ca232 100644
--- a/build.gradle
+++ b/build.gradle
@@ -54,6 +54,12 @@ dependencies {
 
     implementation 'com.google.guava:guava:30.1.1-jre'
 
+    // AFU is an "includedBuild" imported in settings.gradle, so the version number doesn't matter.
+    // https://docs.gradle.org/current/userguide/composite_builds.html#settings_defined_composite
+    implementation('org.checkerframework:annotation-file-utilities:*') {
+        exclude group: 'com.google.errorprone', module: 'javac'
+    }
+
     // Serialize constraints
     implementation 'com.googlecode.json-simple:json-simple:1.1.1'
     // Pretty print serialized constraints
diff --git a/settings.gradle b/settings.gradle
new file mode 100644
index 00000000..054e3af5
--- /dev/null
+++ b/settings.gradle
@@ -0,0 +1,7 @@
+includeBuild ('../annotation-tools/annotation-file-utilities') {
+    if (!file('../annotation-tools/annotation-file-utilities').exists()) {
+        exec {
+            executable '.ci-build-without-test.sh'
+        }
+    }
+}
diff --git a/src/checkers/inference/InferenceAnnotatedTypeFactory.java b/src/checkers/inference/InferenceAnnotatedTypeFactory.java
index c069ef68..d7e30a84 100644
--- a/src/checkers/inference/InferenceAnnotatedTypeFactory.java
+++ b/src/checkers/inference/InferenceAnnotatedTypeFactory.java
@@ -273,7 +273,7 @@ protected void postDirectSuperTypes(AnnotatedTypeMirror type, List<? extends Ann
         Set<AnnotationMirror> annotations = type.getEffectiveAnnotations();
         for (AnnotatedTypeMirror supertype : supertypes) {
             if (!annotations.equals(supertype.getEffectiveAnnotations())) {
-                supertype.clearPrimaryAnnotations();
+                supertype.clearAnnotations();
                 supertype.addAnnotations(annotations);
             }
         }
diff --git a/src/checkers/inference/VariableAnnotator.java b/src/checkers/inference/VariableAnnotator.java
index b73f39ce..445225f7 100644
--- a/src/checkers/inference/VariableAnnotator.java
+++ b/src/checkers/inference/VariableAnnotator.java
@@ -410,7 +410,7 @@ private void addExistentialVariable(final AnnotatedTypeVariable typeVar, final T
         if (elementToAtm.containsKey(varElem)
          && !isUpperBoundOfTypeParam
          && !isReturn) {
-            typeVar.clearPrimaryAnnotations();
+            typeVar.clearAnnotations();
             annotateElementFromStore(varElem, typeVar);
             return;
         }
@@ -420,7 +420,7 @@ private void addExistentialVariable(final AnnotatedTypeVariable typeVar, final T
             potentialVariable = treeToVarAnnoPair.get(typeTree).first;
             // might have a primary annotation lingering around
             // (that would removed in the else clause)
-            typeVar.clearPrimaryAnnotations();
+            typeVar.clearAnnotations();
 
         } else {
             // element from use and see if we already have this as a local var or field?
@@ -431,7 +431,7 @@ private void addExistentialVariable(final AnnotatedTypeVariable typeVar, final T
                                            + "typeVar=" + typeVar + "\n"
                                            + "tree=" + tree + "\n");
                 }
-                typeVar.clearPrimaryAnnotations();
+                typeVar.clearAnnotations();
             }
 
             potentialVariable = createVariable(typeTree);
@@ -1546,7 +1546,7 @@ public void handleBinaryTree(AnnotatedTypeMirror atm, BinaryTree binaryTree) {
             Set<? extends AnnotationMirror> lubs = inferenceTypeFactory
                     .getQualifierHierarchy().leastUpperBounds(a.getEffectiveAnnotations(),
                             b.getEffectiveAnnotations());
-            atm.clearPrimaryAnnotations();
+            atm.clearAnnotations();
             atm.addAnnotations(lubs);
             if (slotManager.getSlot(atm) instanceof VariableSlot) {
                 final Pair<Slot, Set<? extends AnnotationMirror>> varATMPair = Pair.<Slot, Set<? extends AnnotationMirror>>of(
diff --git a/src/checkers/inference/util/CopyUtil.java b/src/checkers/inference/util/CopyUtil.java
index 6efc0370..5f30844a 100644
--- a/src/checkers/inference/util/CopyUtil.java
+++ b/src/checkers/inference/util/CopyUtil.java
@@ -50,7 +50,7 @@ public static class ClearAndCopy implements CopyMethod {
          */
         @Override
         public void copy(AnnotatedTypeMirror from, AnnotatedTypeMirror to) {
-            to.clearPrimaryAnnotations();
+            to.clearAnnotations();
             to.addAnnotations(from.getAnnotations());
         }
     }
@@ -80,7 +80,7 @@ public static void copyParameterReceiverAndReturnTypes(final AnnotatedExecutable
         // TODO: Constructor receivers might be null?
         if (from.getReceiverType() != null && to.getReceiverType() != null) {
             // Only the primary does anything at the moment, so no deep copy.
-            to.getReceiverType().clearPrimaryAnnotations();
+            to.getReceiverType().clearAnnotations();
             to.getReceiverType().addAnnotations(from.getReceiverType().getAnnotations());
         }
 
diff --git a/src/checkers/inference/util/InferenceUtil.java b/src/checkers/inference/util/InferenceUtil.java
index 6d5b5102..a985ce67 100644
--- a/src/checkers/inference/util/InferenceUtil.java
+++ b/src/checkers/inference/util/InferenceUtil.java
@@ -40,7 +40,7 @@ public static Set<AnnotationMirror> clearAnnos(final AnnotatedTypeMirror atm) {
         final Set<AnnotationMirror> oldAnnos = AnnotationUtils.createAnnotationSet();
         oldAnnos.addAll(atm.getAnnotations());
 
-        atm.clearPrimaryAnnotations();
+        atm.clearAnnotations();
         return oldAnnos;
     }