fix(agent): Append runtime JAR to bootstrap class loader

The AppMap runtime JAR must be appended to the bootstrap class loader
search path. This ensures that core AppMap runtime classes, such as
`HookFunctions`, are available to all application classes, regardless
of the specific class loader (e.g., in web servers like Tomcat). This
change fixes `NoClassDefFoundError` issues for `HookFunctions`.

This commit also adds a new `gretty-tomcat` test to verify the fix
in a servlet environment.

Author: dividedmind

agent/src/main/java/com/appland/appmap/Agent.java

@@ -213,13 +213,14 @@ private static void setupRuntime(Path agentJarPath, JarFile agentJar, Instrument
       System.exit(1);
     }
 
-    // Adding the runtime jar to the boot class loader means the classes it
-    // contains will be available everywhere. This avoids issues caused by any
-    // filtering the app's class loader might be doing (e.g. the Scala runtime
-    // when running a Play app).
+    // It's critical to append the runtime JAR to the bootstrap class loader
+    // search path, not the system class loader search path. This ensures that
+    // AppMap's core runtime classes, such as HookFunctions, are available to
+    // all application classes, including those loaded by different class loaders
+    // (e.g., in web servers like Tomcat or other complex environments), which
+    // fixes `NoClassDefFoundError` for `HookFunctions`.
     JarFile runtimeJar = new JarFile(runtimeJarPath.toFile());
-    inst.appendToSystemClassLoaderSearch(runtimeJar);
-    // inst.appendToBootstrapClassLoaderSearch(runtimeJar);
+    inst.appendToBootstrapClassLoaderSearch(runtimeJar);
 
     // HookFunctions can only be referenced after the runtime jar has been
     // appended to the boot class loader.

agent/test/gretty-tomcat/appmap.yml

@@ -0,0 +1,3 @@
+name: gretty-tomcat
+packages:
+- path: org.example

agent/test/gretty-tomcat/build.gradle

@@ -0,0 +1,27 @@
+plugins {
+  id 'war'
+  id 'org.gretty' version '4.1.6'
+}
+
+repositories {
+  mavenCentral()
+}
+
+def appmapJar = System.env.AGENT_JAR
+
+gretty {
+  servletContainer = 'tomcat10'
+  contextPath = '/'
+  jvmArgs = [
+    "-Dappmap.config.file=appmap.yml",
+    "-Dappmap.debug.file=../../build/logs/gretty-tomcat-appmap.log"
+  ]
+  if (appmapJar) {
+      jvmArgs << "-javaagent:${appmapJar}"
+  }
+}
+
+dependencies {
+  providedCompile 'jakarta.servlet:jakarta.servlet-api:5.0.0'
+}
+

agent/test/gretty-tomcat/gretty-tomcat.bats

@@ -0,0 +1,35 @@
+#!/usr/bin/env bats
+
+load '../helper'
+
+setup_file() {
+  cd "${BATS_TEST_DIRNAME}" || exit 1
+  mkdir -p ../build/log
+
+  export LOG="../build/log/gretty-tomcat.log"
+  export SERVER_PORT=8080
+  export WS_URL="http://localhost:${SERVER_PORT}/hello"
+  
+  _configure_logging
+
+  echo -n "Starting gretty-tomcat test server..." >&3
+  gradlew appStart -Pgretty.httpPort=${SERVER_PORT} &> $LOG &
+  export WS_PID=$!
+
+  wait_for_ws
+}
+
+teardown_file() {
+  gradlew appStop || true
+  # stop_ws might fail if /exit is not there, but it also waits for process to die.
+  # We can try to just kill the gradle process if it's still running.
+  kill "$WS_PID" || true
+}
+
+@test "hello world" {
+  run _curl -sXGET "${WS_URL}"
+  assert_success
+  assert_output "Hello, World!"
+}
+
+

agent/test/gretty-tomcat/settings.gradle

@@ -0,0 +1 @@
+rootProject.name = 'gretty-tomcat'

agent/test/gretty-tomcat/src/main/java/org/example/HelloServlet.java

@@ -0,0 +1,15 @@
+package org.example;
+
+import java.io.IOException;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
+
+@WebServlet(name = "HelloServlet", urlPatterns = {"/hello"})
+public class HelloServlet extends HttpServlet {
+    protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+        response.getWriter().print("Hello, World!");
+    }
+}

agent/test/gretty-tomcat/src/main/java/org/example/MyClass.java

@@ -0,0 +1,5 @@
+package org.example;
+
+public class MyClass implements Comparable<MyClass> {
+    public int compareTo(MyClass other) { return 0; }
+}