Fix: disable custom hooks during coverage report generation

src/main/java/com/code_intelligence/jazzer/agent/Agent.kt

@@ -50,6 +50,17 @@ fun installInternal(
     dumpClassesDir: String = Opt.dumpClassesDir.get(),
     additionalClassesExcludes: List<String> = Opt.additionalClassesExcludes.get(),
 ) {
+    // Enable conditional hooks when custom hooks are used together with coverage reporting so
+    // that hooks can be disabled during coverage report generation at shutdown (see #878).
+    // Without this, any use of hooked classes during coverage dumping would trigger custom hook
+    // dispatch, causing NoClassDefFoundError when the hook class is no longer loadable.
+    val useConditionalHooks =
+        conditionalHooks ||
+            (
+                userHookNames.isNotEmpty() &&
+                    (Opt.coverageDump.get().isNotEmpty() || Opt.coverageReport.get().isNotEmpty())
+            )
+
     val allCustomHookNames = (Constants.SANITIZER_HOOK_NAMES + userHookNames).toSet()
     check(allCustomHookNames.isNotEmpty()) { "No hooks registered; expected at least the built-in hooks" }
     val customHookNames = allCustomHookNames - disabledHookNames.toSet()
@@ -136,7 +147,7 @@ fun installInternal(
             instrumentationTypes,
             includedHooks.hooks,
             customHooks.hooks,
-            conditionalHooks,
+            useConditionalHooks,
             customHooks.additionalHookClassNameGlobber,
             coverageIdSynchronizer,
             dumpClassesDirPath,

src/main/java/com/code_intelligence/jazzer/driver/FuzzTargetRunner.java

@@ -448,6 +448,7 @@ public static void registerFatalFindingHandlerForJUnit(Consumer<Throwable> findi
 
   private static void shutdown() {
     if (!Opt.coverageDump.get().isEmpty() || !Opt.coverageReport.get().isEmpty()) {
+      JazzerInternal.hooksEnabled = false;
       if (!Opt.coverageDump.get().isEmpty()) {
         CoverageRecorder.dumpJacocoCoverage(Opt.coverageDump.get());
       }

src/main/java/com/code_intelligence/jazzer/driver/Opt.java

@@ -250,7 +250,8 @@ public final class Opt {
   public static final OptItem<Boolean> mergeInner = boolSetting("merge_inner", false, null);
 
   // Whether hook instrumentation should add a check for JazzerInternal#hooksEnabled before
-  // executing hooks. Used to disable hooks during non-fuzz JUnit tests.
+  // executing hooks. Used to disable hooks during non-fuzz JUnit tests and during coverage
+  // report generation at shutdown.
   public static final OptItem<Boolean> conditionalHooks =
       boolSetting("conditional_hooks", false, null);
 

tests/BUILD.bazel

@@ -124,6 +124,32 @@ java_fuzz_target_test(
     ],
 )
 
+java_binary(
+    name = "CoverageWithHooksFuzzerHooks",
+    srcs = ["src/test/java/com/example/CoverageWithHooksFuzzerHooks.java"],
+    create_executable = False,
+    deploy_manifest_lines = ["Jazzer-Hook-Classes: com.example.CoverageWithHooksFuzzerHooks"],
+    deps = ["//src/main/java/com/code_intelligence/jazzer/api:hooks"],
+)
+
+# Regression test for https://github.com/CodeIntelligence/jazzer/issues/878:
+# Custom hooks must be disabled during coverage report generation to prevent
+# NoClassDefFoundError when hooked classes are used and the hook class is no
+# longer available.
+java_fuzz_target_test(
+    name = "CoverageWithHooksFuzzer",
+    srcs = ["src/test/java/com/example/CoverageWithHooksFuzzer.java"],
+    allowed_findings = ["com.code_intelligence.jazzer.api.FuzzerSecurityIssueLow"],
+    fuzzer_args = [
+        "--coverage_report=coverage.txt",
+        "--instrumentation_includes=com.example.**",
+    ],
+    hook_jar = "CoverageWithHooksFuzzerHooks_deploy.jar",
+    target_class = "com.example.CoverageWithHooksFuzzer",
+    verify_crash_input = False,
+    verify_crash_reproducer = False,
+)
+
 java_library(
     name = "autofuzz_inner_class_target",
     srcs = ["src/test/java/com/example/AutofuzzInnerClassTarget.java"],

tests/src/test/java/com/example/CoverageWithHooksFuzzer.java

@@ -0,0 +1,62 @@
+/*
+ * Copyright 2026 Code Intelligence GmbH
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package com.example;
+
+import com.code_intelligence.jazzer.api.FuzzerSecurityIssueLow;
+import java.util.ArrayList;
+
+/**
+ * Regression test for https://github.com/CodeIntelligence/jazzer/issues/878.
+ *
+ * <p>When generating a coverage report at shutdown, any use of hooked method would trigger custom
+ * hook dispatch. If the hook class is no longer loadable at that point, the JVM throws
+ * NoClassDefFoundError.
+ *
+ * <p>This test verifies that hooks are disabled during coverage report generation by checking
+ * whether the hook's system property marker was set after the last fuzzer iteration. The shutdown
+ * sequence calls coverage report generation BEFORE fuzzerTearDown, so if hooks fire during report
+ * generation, the property will be set when fuzzerTearDown runs.
+ */
+public class CoverageWithHooksFuzzer {
+  public static void fuzzerTestOneInput(byte[] data) {
+    // Use ArrayList so the hook fires during fuzzing.
+    ArrayList<Byte> list = new ArrayList<>();
+    for (byte b : data) {
+      list.add(b);
+    }
+    // Verify the hook actually fired during this iteration.
+    if (!"true".equals(System.getProperty("jazzer.test.hook.called"))) {
+      throw new IllegalStateException("Hook did not fire during fuzzing");
+    }
+    // Clear the property after all ArrayList usage in this iteration.
+    // If hooks fire during coverage report generation (after the last iteration),
+    // the property will be set again.
+    System.clearProperty("jazzer.test.hook.called");
+    if (list.size() > 3) {
+      throw new FuzzerSecurityIssueLow("found enough bytes");
+    }
+  }
+
+  public static void fuzzerTearDown() {
+    // fuzzerTearDown is called AFTER coverage report generation in the shutdown sequence.
+    // If hooks were active during coverage report generation, use of hooked classes
+    // would have triggered our hook, setting the property.
+    if ("true".equals(System.getProperty("jazzer.test.hook.called"))) {
+      throw new IllegalStateException("Hook was called during coverage report generation");
+    }
+  }
+}

tests/src/test/java/com/example/CoverageWithHooksFuzzerHooks.java

@@ -0,0 +1,36 @@
+/*
+ * Copyright 2026 Code Intelligence GmbH
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package com.example;
+
+import com.code_intelligence.jazzer.api.HookType;
+import com.code_intelligence.jazzer.api.MethodHook;
+import java.lang.invoke.MethodHandle;
+
+/**
+ * Hook that targets ArrayList.<init> that sets a system property so that we can check in the
+ * fuzz test whether the hook is called or not.
+ */
+public class CoverageWithHooksFuzzerHooks {
+  @MethodHook(
+      type = HookType.AFTER,
+      targetClassName = "java.util.ArrayList",
+      targetMethod = "<init>")
+  public static void arrayListInitHook(
+      MethodHandle method, Object thisObject, Object[] arguments, int hookId, Object returnValue) {
+    System.setProperty("jazzer.test.hook.called", "true");
+  }
+}