diff --git a/core/src/main/java/org/elasticsearch/bootstrap/JarHell.java b/core/src/main/java/org/elasticsearch/bootstrap/JarHell.java
index fecc370f748..dac62415549 100644
--- a/core/src/main/java/org/elasticsearch/bootstrap/JarHell.java
+++ b/core/src/main/java/org/elasticsearch/bootstrap/JarHell.java
@@ -46,6 +46,11 @@ import java.util.jar.Manifest;
 /** Simple check for duplicate class files across the classpath */
 public class JarHell {
 
+    /** Simple driver class, can be used eg. from builds. Returns non-zero on jar-hell */
+    public static void main(String args[]) throws Exception {
+        checkJarHell();
+    }
+
     /**
      * Checks the current classloader for duplicate classes
      * @throws IllegalStateException if jar hell was found
@@ -57,9 +62,9 @@ public class JarHell {
         }
         ESLogger logger = Loggers.getLogger(JarHell.class);
         if (logger.isDebugEnabled()) {
-            logger.debug("java.class.path= {}" + System.getProperty("java.class.path"));
-            logger.debug("sun.boot.class.path= {}" + System.getProperty("sun.boot.class.path"));
-            logger.debug("classloader urls= {}" + Arrays.toString(((URLClassLoader)loader).getURLs()));
+            logger.debug("java.class.path: {}", System.getProperty("java.class.path"));
+            logger.debug("sun.boot.class.path: {}", System.getProperty("sun.boot.class.path"));
+            logger.debug("classloader urls: {}", Arrays.toString(((URLClassLoader)loader).getURLs()));
         }
         checkJarHell(((URLClassLoader)loader).getURLs());
     }
@@ -70,14 +75,27 @@ public class JarHell {
      */
     @SuppressForbidden(reason = "needs JarFile for speed, just reading entries")
     public static void checkJarHell(URL urls[]) throws Exception {
+        ESLogger logger = Loggers.getLogger(JarHell.class);
+        // we don't try to be sneaky and use deprecated/internal/not portable stuff
+        // like sun.boot.class.path, and with jigsaw we don't yet have a way to get
+        // a "list" at all. So just exclude any elements underneath the java home
+        String javaHome = System.getProperty("java.home");
+        logger.debug("java.home: {}", javaHome);
         final Map<String,URL> clazzes = new HashMap<>(32768);
         Set<String> seenJars = new HashSet<>();
         for (final URL url : urls) {
             String path = URLDecoder.decode(url.getPath(), "UTF-8");
+            // exclude system resources
+            if (path.startsWith(javaHome)) {
+                logger.debug("excluding system resource: {}", path);
+                continue;
+            }
             if (path.endsWith(".jar")) {
                 if (!seenJars.add(path)) {
+                    logger.debug("excluding duplicate classpath element: {}", path);
                     continue; // we can't fail because of sheistiness with joda-time
                 }
+                logger.debug("examining jar: {}", path);
                 try (JarFile file = new JarFile(path)) {
                     Manifest manifest = file.getManifest();
                     if (manifest != null) {
@@ -111,6 +129,7 @@ public class JarHell {
                     }
                 }
             } else {
+                logger.debug("examining directory: {}", path);
                 // case for tests: where we have class files in the classpath
                 final Path root = PathUtils.get(url.toURI());
                 final String sep = root.getFileSystem().getSeparator();
diff --git a/core/src/test/java/org/elasticsearch/bootstrap/BootstrapForTesting.java b/core/src/test/java/org/elasticsearch/bootstrap/BootstrapForTesting.java
index 1fbb1462ac6..e73805ff995 100644
--- a/core/src/test/java/org/elasticsearch/bootstrap/BootstrapForTesting.java
+++ b/core/src/test/java/org/elasticsearch/bootstrap/BootstrapForTesting.java
@@ -25,6 +25,7 @@ import org.elasticsearch.bootstrap.ESPolicy;
 import org.elasticsearch.bootstrap.Security;
 import org.elasticsearch.common.Strings;
 import org.elasticsearch.common.io.PathUtils;
+import org.elasticsearch.common.logging.Loggers;
 
 import java.io.FilePermission;
 import java.nio.file.Path;
@@ -55,7 +56,13 @@ public class BootstrapForTesting {
         try {
             JarHell.checkJarHell();
         } catch (Exception e) {
-            throw new RuntimeException("found jar hell in test classpath", e);
+            if (Boolean.parseBoolean(System.getProperty("tests.maven"))) {
+                throw new RuntimeException("found jar hell in test classpath", e);
+            } else {
+                Loggers.getLogger(BootstrapForTesting.class)
+                    .warn("Your ide or custom test runner has jar hell issues, " +
+                          "you might want to look into that", e);
+            }
         }
 
         // make sure java.io.tmpdir exists always (in case code uses it in a static initializer)