diff --git a/compiler/src/jdk.graal.compiler/src/jdk/graal/compiler/util/json/JsonPrettyWriter.java b/compiler/src/jdk.graal.compiler/src/jdk/graal/compiler/util/json/JsonPrettyWriter.java
index 7c6cb66264dc..15f1f8abf2bd 100644
--- a/compiler/src/jdk.graal.compiler/src/jdk/graal/compiler/util/json/JsonPrettyWriter.java
+++ b/compiler/src/jdk.graal.compiler/src/jdk/graal/compiler/util/json/JsonPrettyWriter.java
@@ -26,6 +26,7 @@
 
 import java.io.IOException;
 import java.io.Writer;
+import java.nio.file.Path;
 
 /**
  * Subclass of {@link JsonWriter} that pretty-prints its output. More specifically, a newline will
@@ -42,6 +43,10 @@ public JsonPrettyWriter(Writer writer) {
         super(writer);
     }
 
+    public JsonPrettyWriter(Path path) throws IOException {
+        super(path);
+    }
+
     @Override
     public JsonWriter appendObjectStart() throws IOException {
         return super.appendObjectStart().indent().newline();
@@ -53,6 +58,17 @@ public JsonWriter appendObjectEnd() throws IOException {
         return super.appendObjectEnd();
     }
 
+    @Override
+    public JsonWriter appendArrayStart() throws IOException {
+        return super.appendArrayStart().indent().newline();
+    }
+
+    @Override
+    public JsonWriter appendArrayEnd() throws IOException {
+        unindent().newline();
+        return super.appendArrayEnd();
+    }
+
     @Override
     public JsonWriter appendFieldSeparator() throws IOException {
         return super.appendFieldSeparator().append(' ');
diff --git a/compiler/src/jdk.graal.compiler/src/jdk/graal/compiler/util/json/JsonPrinter.java b/compiler/src/jdk.graal.compiler/src/jdk/graal/compiler/util/json/JsonPrinter.java
index cef066f2dc0b..949554a9a9de 100644
--- a/compiler/src/jdk.graal.compiler/src/jdk/graal/compiler/util/json/JsonPrinter.java
+++ b/compiler/src/jdk.graal.compiler/src/jdk/graal/compiler/util/json/JsonPrinter.java
@@ -55,6 +55,11 @@ public interface JsonPrinter<T> {
      * @see JsonWriter#print(Object)
      */
     static <T> void printCollection(JsonWriter writer, Collection<T> collection, Comparator<T> comparator, JsonPrinter<T> elementPrinter) throws IOException {
+        if (collection.isEmpty()) {
+            writer.append("[]");
+            return;
+        }
+
         Collection<T> ordered = collection;
         if (comparator != null) {
             ordered = new ArrayList<>(collection);
diff --git a/substratevm/src/com.oracle.svm.agent/src/com/oracle/svm/agent/NativeImageAgent.java b/substratevm/src/com.oracle.svm.agent/src/com/oracle/svm/agent/NativeImageAgent.java
index 14c74345636e..22f58014f64f 100644
--- a/substratevm/src/com.oracle.svm.agent/src/com/oracle/svm/agent/NativeImageAgent.java
+++ b/substratevm/src/com.oracle.svm.agent/src/com/oracle/svm/agent/NativeImageAgent.java
@@ -75,6 +75,7 @@
 import com.oracle.svm.configure.trace.AccessAdvisor;
 import com.oracle.svm.configure.trace.TraceProcessor;
 import com.oracle.svm.core.configure.ConfigurationFile;
+import com.oracle.svm.core.configure.PredefinedClassesConfigurationParser;
 import com.oracle.svm.core.jni.headers.JNIEnvironment;
 import com.oracle.svm.core.jni.headers.JNIJavaVM;
 import com.oracle.svm.core.jni.headers.JNIObjectHandle;
@@ -86,6 +87,8 @@
 import com.oracle.svm.jvmtiagentbase.jvmti.JvmtiEventCallbacks;
 import com.oracle.svm.jvmtiagentbase.jvmti.JvmtiInterface;
 
+import jdk.graal.compiler.phases.common.LazyValue;
+
 public final class NativeImageAgent extends JvmtiAgentBase<NativeImageAgentJNIHandleSet> {
     private static final String AGENT_NAME = "native-image-agent";
     private static final TimeZone UTC_TIMEZONE = TimeZone.getTimeZone("UTC");
@@ -338,7 +341,7 @@ protected int onLoadCallback(JNIJavaVM vm, JvmtiEnv jvmti, JvmtiEventCallbacks c
                         tracingResultWriter = new ConfigurationWithOriginsWriter(configWithOriginsTracer);
                     }
                 } else {
-                    Path[] predefinedClassDestDirs = {Files.createDirectories(configOutputDirPath.resolve(ConfigurationFile.PREDEFINED_CLASSES_AGENT_EXTRACTED_SUBDIR))};
+                    List<LazyValue<Path>> predefinedClassDestDirs = List.of(PredefinedClassesConfigurationParser.directorySupplier(configOutputDirPath));
                     Function<IOException, Exception> handler = e -> {
                         if (e instanceof NoSuchFileException) {
                             warn("file " + ((NoSuchFileException) e).getFile() + " for merging could not be found, skipping");
@@ -543,9 +546,11 @@ private void writeConfigurationFiles() {
                 throw unexpectedlyModified(configOutputLockFilePath);
             }
             expectUnmodified(configOutputLockFilePath);
-            if (!mostRecent.equals(expectedConfigModifiedBefore)) {
-                throw unexpectedlyModified(configOutputDirPath);
-            }
+            /*
+             * Checking for the modification of the whole configuration directory is not possible
+             * since predefined classes configuration outputs folders and files during the agent
+             * run.
+             */
 
             Path[] targetFilePaths = new Path[tempFilePaths.size()];
             for (int i = 0; i < tempFilePaths.size(); i++) {
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/command/ConfigurationGenerateCommand.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/command/ConfigurationGenerateCommand.java
index 53e688d55772..b19a215fe8c6 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/command/ConfigurationGenerateCommand.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/command/ConfigurationGenerateCommand.java
@@ -46,9 +46,11 @@
 import com.oracle.svm.configure.filters.HierarchyFilterNode;
 import com.oracle.svm.configure.trace.AccessAdvisor;
 import com.oracle.svm.configure.trace.TraceProcessor;
-import com.oracle.svm.core.configure.ConfigurationFile;
+import com.oracle.svm.core.configure.PredefinedClassesConfigurationParser;
 import com.oracle.svm.util.LogUtils;
 
+import jdk.graal.compiler.phases.common.LazyValue;
+
 public class ConfigurationGenerateCommand extends ConfigurationCommand {
     @Override
     public String getName() {
@@ -264,14 +266,12 @@ protected static void generate(Iterator<String> argumentsIterator, boolean accep
 
         try {
             omittedConfigurationSet = omittedCollection.loadConfigurationSet(ConfigurationFileCollection.FAIL_ON_EXCEPTION, null, null);
-            List<Path> predefinedClassDestDirs = new ArrayList<>();
+            List<LazyValue<Path>> predefinedClassDestDirs = new ArrayList<>();
             for (URI pathUri : outputCollection.getPredefinedClassesConfigPaths()) {
-                Path subdir = Files.createDirectories(Paths.get(pathUri).getParent().resolve(ConfigurationFile.PREDEFINED_CLASSES_AGENT_EXTRACTED_SUBDIR));
-                subdir = Files.createDirectories(subdir);
-                predefinedClassDestDirs.add(subdir);
+                predefinedClassDestDirs.add(PredefinedClassesConfigurationParser.directorySupplier(Paths.get(pathUri).getParent()));
             }
             Predicate<String> shouldExcludeClassesWithHash = omittedConfigurationSet.getPredefinedClassesConfiguration()::containsClassWithHash;
-            configurationSet = inputCollection.loadConfigurationSet(ConfigurationFileCollection.FAIL_ON_EXCEPTION, predefinedClassDestDirs.toArray(new Path[0]), shouldExcludeClassesWithHash);
+            configurationSet = inputCollection.loadConfigurationSet(ConfigurationFileCollection.FAIL_ON_EXCEPTION, predefinedClassDestDirs, shouldExcludeClassesWithHash);
         } catch (IOException e) {
             throw e;
         } catch (Throwable t) {
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationConditionPrintable.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationConditionPrintable.java
index 259d861e285c..d9a4eda47730 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationConditionPrintable.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationConditionPrintable.java
@@ -37,9 +37,9 @@
 final class ConfigurationConditionPrintable {
     static void printConditionAttribute(UnresolvedConfigurationCondition condition, JsonWriter writer) throws IOException {
         if (!condition.isAlwaysTrue()) {
-            writer.quote(CONDITIONAL_KEY).append(":{");
-            writer.quote(condition.isRuntimeChecked() ? TYPE_REACHED_KEY : TYPE_REACHABLE_KEY).append(':').quote(condition.getTypeName());
-            writer.append("},").newline();
+            writer.quote(CONDITIONAL_KEY).appendFieldSeparator().appendObjectStart();
+            writer.quote(condition.isRuntimeChecked() ? TYPE_REACHED_KEY : TYPE_REACHABLE_KEY).appendFieldSeparator().quote(condition.getTypeName());
+            writer.appendObjectEnd().appendSeparator();
         }
     }
 }
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationFileCollection.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationFileCollection.java
index cf2fc9046ad6..a6310afb98db 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationFileCollection.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationFileCollection.java
@@ -35,6 +35,7 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedHashSet;
+import java.util.List;
 import java.util.Objects;
 import java.util.Set;
 import java.util.function.Function;
@@ -44,6 +45,7 @@
 import com.oracle.svm.core.configure.ConfigurationFile;
 import com.oracle.svm.core.configure.ConfigurationParser;
 import com.oracle.svm.core.util.VMError;
+import jdk.graal.compiler.phases.common.LazyValue;
 
 public class ConfigurationFileCollection {
     public static final Function<IOException, Exception> FAIL_ON_EXCEPTION = e -> e;
@@ -161,7 +163,7 @@ public ProxyConfiguration loadProxyConfig(Function<IOException, Exception> excep
         return proxyConfiguration;
     }
 
-    public PredefinedClassesConfiguration loadPredefinedClassesConfig(Path[] classDestinationDirs, Predicate<String> shouldExcludeClassesWithHash,
+    public PredefinedClassesConfiguration loadPredefinedClassesConfig(List<LazyValue<Path>> classDestinationDirs, Predicate<String> shouldExcludeClassesWithHash,
                     Function<IOException, Exception> exceptionHandler) throws Exception {
         PredefinedClassesConfiguration predefinedClassesConfiguration = new PredefinedClassesConfiguration(classDestinationDirs, shouldExcludeClassesWithHash);
         loadConfig(predefinedClassesConfigPaths, predefinedClassesConfiguration.createParser(false), exceptionHandler);
@@ -182,7 +184,7 @@ public SerializationConfiguration loadSerializationConfig(Function<IOException,
         return serializationConfiguration;
     }
 
-    public ConfigurationSet loadConfigurationSet(Function<IOException, Exception> exceptionHandler, Path[] predefinedConfigClassDestinationDirs,
+    public ConfigurationSet loadConfigurationSet(Function<IOException, Exception> exceptionHandler, List<LazyValue<Path>> predefinedConfigClassDestinationDirs,
                     Predicate<String> predefinedConfigClassWithHashExclusionPredicate) throws Exception {
         return new ConfigurationSet(loadReflectConfig(exceptionHandler), loadJniConfig(exceptionHandler), loadResourceConfig(exceptionHandler), loadProxyConfig(exceptionHandler),
                         loadSerializationConfig(exceptionHandler),
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationMethod.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationMethod.java
index 858d2bcc52dc..e66390d2733a 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationMethod.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationMethod.java
@@ -25,6 +25,7 @@
 package com.oracle.svm.configure.config;
 
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Objects;
 
@@ -85,15 +86,10 @@ public boolean isConstructor() {
 
     @Override
     public void printJson(JsonWriter writer) throws IOException {
-        writer.append('{');
-        writer.quote("name").append(':').quote(name).append(',');
-        writer.quote("parameterTypes").append(":[");
-        String prefix = "";
-        for (String type : SignatureUtil.toParameterTypes(internalSignature)) {
-            writer.append(prefix).quote(type);
-            prefix = ",";
-        }
-        writer.append("] }");
+        writer.appendObjectStart();
+        writer.quote("name").appendFieldSeparator().quote(name).appendSeparator();
+        writer.quote("parameterTypes").appendFieldSeparator().print(Arrays.asList(SignatureUtil.toParameterTypes(internalSignature)));
+        writer.appendObjectEnd();
     }
 
     @Override
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationSet.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationSet.java
index 6c5539f2ee3b..5e3211f488b7 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationSet.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationSet.java
@@ -40,6 +40,7 @@
 import com.oracle.svm.core.configure.ConfigurationFile;
 import com.oracle.svm.core.util.VMError;
 
+import jdk.graal.compiler.util.json.JsonPrettyWriter;
 import jdk.graal.compiler.util.json.JsonPrintable;
 import jdk.graal.compiler.util.json.JsonWriter;
 
@@ -71,9 +72,10 @@ public ConfigurationSet(ConfigurationSet other) {
                         other.predefinedClassesConfiguration.copy());
     }
 
+    @SuppressWarnings("unchecked")
     public ConfigurationSet() {
         this(new TypeConfiguration(REFLECTION_KEY), new TypeConfiguration(JNI_KEY), new ResourceConfiguration(), new ProxyConfiguration(), new SerializationConfiguration(),
-                        new PredefinedClassesConfiguration(new Path[0], hash -> false));
+                        new PredefinedClassesConfiguration(Collections.emptyList(), hash -> false));
     }
 
     private ConfigurationSet mutate(ConfigurationSet other, Mutator mutator) {
@@ -161,8 +163,8 @@ public static List<Path> writeConfigurationToAllPaths(Function<ConfigurationFile
         ConfigurationFile reachabilityMetadataFile = ConfigurationFile.REACHABILITY_METADATA;
         for (Path path : configFilePathResolver.apply(reachabilityMetadataFile)) {
             writtenFiles.add(path);
-            JsonWriter writer = new JsonWriter(path);
-            writer.appendObjectStart().indent().newline();
+            JsonWriter writer = new JsonPrettyWriter(path);
+            writer.appendObjectStart();
             boolean first = true;
             for (ConfigurationFile configFile : ConfigurationFile.agentGeneratedFiles()) {
                 JsonPrintable configuration = configSupplier.apply(configFile);
@@ -178,10 +180,14 @@ public static List<Path> writeConfigurationToAllPaths(Function<ConfigurationFile
                         }
                     }
                 } else {
+                    if (configuration instanceof ConfigurationBase<?, ?> configurationBase && configurationBase.isEmpty()) {
+                        /* Do not add an empty field when there are no entries */
+                        continue;
+                    }
                     if (first) {
                         first = false;
                     } else {
-                        writer.appendSeparator().newline();
+                        writer.appendSeparator();
                     }
                     if (!configFile.equals(ConfigurationFile.RESOURCES)) {
                         /*
@@ -193,7 +199,7 @@ public static List<Path> writeConfigurationToAllPaths(Function<ConfigurationFile
                     configSupplier.apply(configFile).printJson(writer);
                 }
             }
-            writer.unindent().newline().appendObjectEnd();
+            writer.appendObjectEnd();
             writer.close();
         }
         return writtenFiles;
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationType.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationType.java
index cca24a998ccc..7284a8120bf9 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationType.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ConfigurationType.java
@@ -39,15 +39,13 @@
 
 import com.oracle.svm.configure.config.ConfigurationMemberInfo.ConfigurationMemberAccessibility;
 import com.oracle.svm.configure.config.ConfigurationMemberInfo.ConfigurationMemberDeclaration;
-
 import com.oracle.svm.core.configure.ConfigurationTypeDescriptor;
 
+import jdk.graal.compiler.util.SignatureUtil;
 import jdk.graal.compiler.util.json.JsonPrintable;
 import jdk.graal.compiler.util.json.JsonPrinter;
 import jdk.graal.compiler.util.json.JsonWriter;
 
-import jdk.graal.compiler.util.SignatureUtil;
-
 /**
  * Type usage information, part of a {@link TypeConfiguration}. Unlike other configuration classes
  * like {@link ConfigurationMethod}, this class is not immutable and uses locking to synchronize
@@ -461,9 +459,9 @@ public synchronized void setAllPublicConstructors(ConfigurationMemberAccessibili
 
     @Override
     public synchronized void printJson(JsonWriter writer) throws IOException {
-        writer.append('{').indent().newline();
+        writer.appendObjectStart();
         ConfigurationConditionPrintable.printConditionAttribute(condition, writer);
-        writer.quote("type").append(":");
+        writer.quote("type").appendFieldSeparator();
         typeDescriptor.printJson(writer);
 
         printJsonBooleanIfSet(writer, allDeclaredFieldsAccess == ConfigurationMemberAccessibility.ACCESSED, "allDeclaredFields");
@@ -475,13 +473,13 @@ public synchronized void printJson(JsonWriter writer) throws IOException {
         printJsonBooleanIfSet(writer, unsafeAllocated, "unsafeAllocated");
 
         if (fields != null) {
-            writer.append(',').newline().quote("fields").append(':');
+            writer.appendSeparator().quote("fields").appendFieldSeparator();
             JsonPrinter.printCollection(writer, fields.entrySet(), Map.Entry.comparingByKey(), ConfigurationType::printField);
         }
         if (methods != null) {
             Set<ConfigurationMethod> accessedMethods = getMethodsByAccessibility(ConfigurationMemberAccessibility.ACCESSED);
             if (!accessedMethods.isEmpty()) {
-                writer.append(',').newline().quote("methods").append(':');
+                writer.appendSeparator().quote("methods").appendFieldSeparator();
                 JsonPrinter.printCollection(writer,
                                 accessedMethods,
                                 Comparator.comparing(ConfigurationMethod::getName).thenComparing(Comparator.nullsFirst(Comparator.comparing(ConfigurationMethod::getInternalSignature))),
@@ -489,7 +487,7 @@ public synchronized void printJson(JsonWriter writer) throws IOException {
             }
         }
 
-        writer.unindent().newline().append('}');
+        writer.appendObjectEnd();
     }
 
     private Set<ConfigurationMethod> getMethodsByAccessibility(ConfigurationMemberAccessibility accessibility) {
@@ -497,11 +495,11 @@ private Set<ConfigurationMethod> getMethodsByAccessibility(ConfigurationMemberAc
     }
 
     private static void printField(Map.Entry<String, FieldInfo> entry, JsonWriter w) throws IOException {
-        w.append('{').quote("name").append(':').quote(entry.getKey());
+        w.appendObjectStart().quote("name").appendFieldSeparator().quote(entry.getKey());
         if (entry.getValue().isFinalButWritable()) {
-            w.append(", ").quote("allowWrite").append(':').append("true");
+            w.appendSeparator().quote("allowWrite").appendFieldSeparator().append("true");
         }
-        w.append('}');
+        w.appendObjectEnd();
     }
 
     private static void printJsonBooleanIfSet(JsonWriter writer, boolean predicate, String attribute) throws IOException {
@@ -511,7 +509,7 @@ private static void printJsonBooleanIfSet(JsonWriter writer, boolean predicate,
     }
 
     private static void printJsonBoolean(JsonWriter writer, boolean value, String attribute) throws IOException {
-        writer.append(',').newline().quote(attribute).append(":").append(Boolean.toString(value));
+        writer.appendSeparator().quote(attribute).appendFieldSeparator().append(Boolean.toString(value));
     }
 
     private void removeFields(ConfigurationMemberDeclaration declaration, ConfigurationMemberAccessibility accessibility) {
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/PredefinedClassesConfiguration.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/PredefinedClassesConfiguration.java
index a1ebb57a9e39..2539272cb0c0 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/PredefinedClassesConfiguration.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/PredefinedClassesConfiguration.java
@@ -31,9 +31,11 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
+import java.util.List;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ConcurrentMap;
 
+import jdk.graal.compiler.phases.common.LazyValue;
 import org.graalvm.nativeimage.impl.UnresolvedConfigurationCondition;
 
 import com.oracle.svm.configure.ConfigurationBase;
@@ -46,11 +48,11 @@
 import jdk.graal.compiler.util.json.JsonWriter;
 
 public final class PredefinedClassesConfiguration extends ConfigurationBase<PredefinedClassesConfiguration, PredefinedClassesConfiguration.Predicate> {
-    private final Path[] classDestinationDirs;
+    private final List<LazyValue<Path>> classDestinationDirs;
     private final ConcurrentMap<String, ConfigurationPredefinedClass> classes = new ConcurrentHashMap<>();
     private final java.util.function.Predicate<String> shouldExcludeClassWithHash;
 
-    public PredefinedClassesConfiguration(Path[] classDestinationDirs, java.util.function.Predicate<String> shouldExcludeClassWithHash) {
+    public PredefinedClassesConfiguration(List<LazyValue<Path>> classDestinationDirs, java.util.function.Predicate<String> shouldExcludeClassWithHash) {
         this.classDestinationDirs = classDestinationDirs;
         this.shouldExcludeClassWithHash = shouldExcludeClassWithHash;
     }
@@ -98,9 +100,9 @@ public void add(String nameInfo, byte[] classData) {
             return;
         }
         if (classDestinationDirs != null) {
-            for (Path dir : classDestinationDirs) {
+            for (LazyValue<Path> dir : classDestinationDirs) {
                 try {
-                    Files.write(dir.resolve(getFileName(hash)), classData);
+                    Files.write(dir.get().resolve(getFileName(hash)), classData);
                 } catch (IOException e) {
                     throw new RuntimeException(e);
                 }
@@ -121,11 +123,11 @@ public void add(String nameInfo, String hash, URI baseUri) {
             } catch (Exception ignored) {
                 localBaseDir = null;
             }
-            for (Path destDir : classDestinationDirs) {
-                if (!destDir.equals(localBaseDir)) {
+            for (LazyValue<Path> destDir : classDestinationDirs) {
+                if (!destDir.get().equals(localBaseDir)) {
                     try {
                         String fileName = getFileName(hash);
-                        Path target = destDir.resolve(fileName);
+                        Path target = destDir.get().resolve(fileName);
                         if (baseUri != null) {
                             try (InputStream is = PredefinedClassesConfigurationParser.openClassdataStream(baseUri, hash)) {
                                 Files.copy(is, target, StandardCopyOption.REPLACE_EXISTING);
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ResourceConfiguration.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ResourceConfiguration.java
index 24176fe86d56..50b7ac8199f1 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ResourceConfiguration.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/ResourceConfiguration.java
@@ -352,19 +352,19 @@ public void printLegacyJson(JsonWriter writer) throws IOException {
     }
 
     void printResourcesJson(JsonWriter writer) throws IOException {
-        writer.quote(RESOURCES_KEY).append(':').append('{').indent().newline();
-        writer.quote("includes").append(':');
+        writer.quote(RESOURCES_KEY).appendFieldSeparator().appendObjectStart();
+        writer.quote("includes").appendFieldSeparator();
         JsonPrinter.printCollection(writer, addedResources, ConditionalElement.comparator(), ResourceConfiguration::conditionalRegexElementJson);
         if (!ignoredResources.isEmpty()) {
-            writer.append(',').newline();
-            writer.quote("excludes").append(':');
+            writer.appendSeparator();
+            writer.quote("excludes").appendFieldSeparator();
             JsonPrinter.printCollection(writer, ignoredResources.keySet(), ConditionalElement.comparator(), ResourceConfiguration::conditionalRegexElementJson);
         }
-        writer.unindent().newline().append('}');
+        writer.appendObjectEnd();
     }
 
     void printBundlesJson(JsonWriter writer) throws IOException {
-        writer.quote(BUNDLES_KEY).append(':');
+        writer.quote(BUNDLES_KEY).appendFieldSeparator();
         JsonPrinter.printCollection(writer, bundles.keySet(), ConditionalElement.comparator(), (p, w) -> printResourceBundle(bundles.get(p), w));
     }
 
@@ -379,23 +379,23 @@ public ConfigurationParser createParser(boolean strictMetadata) {
     }
 
     private static void printResourceBundle(BundleConfiguration config, JsonWriter writer) throws IOException {
-        writer.append('{').indent().newline();
+        writer.appendObjectStart();
         ConfigurationConditionPrintable.printConditionAttribute(config.condition, writer);
-        writer.quote("name").append(':').quote(config.baseName);
+        writer.quote("name").appendFieldSeparator().quote(config.baseName);
         if (!config.locales.isEmpty()) {
-            writer.append(',').newline().quote("locales").append(":");
+            writer.appendSeparator().quote("locales").appendFieldSeparator();
             JsonPrinter.printCollection(writer, config.locales, Comparator.naturalOrder(), (String p, JsonWriter w) -> w.quote(p));
         }
         if (!config.classNames.isEmpty()) {
-            writer.append(',').newline().quote("classNames").append(":");
+            writer.appendSeparator().quote("classNames").appendFieldSeparator();
             JsonPrinter.printCollection(writer, config.classNames, Comparator.naturalOrder(), (String p, JsonWriter w) -> w.quote(p));
         }
-        writer.unindent().newline().append('}');
+        writer.appendObjectEnd();
     }
 
     @Override
     public boolean isEmpty() {
-        return addedResources.isEmpty() && bundles.isEmpty();
+        return addedResources.isEmpty() && bundles.isEmpty() && addedGlobs.isEmpty();
     }
 
     @Override
@@ -414,20 +414,20 @@ public boolean supportsCombinedFile() {
     private static void conditionalGlobElementJson(ConditionalElement<ResourceEntry> p, JsonWriter w) throws IOException {
         String pattern = p.element().pattern();
         String module = p.element().module();
-        w.append('{').indent().newline();
+        w.appendObjectStart();
         ConfigurationConditionPrintable.printConditionAttribute(p.condition(), w);
         if (module != null) {
-            w.quote("module").append(':').quote(module).append(',').newline();
+            w.quote("module").appendFieldSeparator().quote(module).appendSeparator();
         }
-        w.quote("glob").append(':').quote(pattern);
-        w.unindent().newline().append('}');
+        w.quote("glob").appendFieldSeparator().quote(pattern);
+        w.appendObjectEnd();
     }
 
     private static void conditionalRegexElementJson(ConditionalElement<String> p, JsonWriter w) throws IOException {
-        w.append('{').indent().newline();
+        w.appendObjectStart();
         ConfigurationConditionPrintable.printConditionAttribute(p.condition(), w);
-        w.quote("pattern").append(':').quote(p.element());
-        w.unindent().newline().append('}');
+        w.quote("pattern").appendFieldSeparator().quote(p.element());
+        w.appendObjectEnd();
     }
 
     public interface Predicate {
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfiguration.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfiguration.java
index 350ff72d715f..438fe8f50ab5 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfiguration.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfiguration.java
@@ -27,7 +27,7 @@
 
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Collections;
+import java.util.Comparator;
 import java.util.List;
 import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
@@ -42,7 +42,7 @@
 import com.oracle.svm.core.configure.SerializationConfigurationParser;
 
 import jdk.graal.compiler.java.LambdaUtils;
-import jdk.graal.compiler.util.json.JsonPrintable;
+import jdk.graal.compiler.util.json.JsonPrinter;
 import jdk.graal.compiler.util.json.JsonWriter;
 
 public final class SerializationConfiguration extends ConfigurationBase<SerializationConfiguration, SerializationConfiguration.Predicate>
@@ -111,26 +111,22 @@ public boolean contains(UnresolvedConfigurationCondition condition, String seria
     @Override
     public void printJson(JsonWriter writer) throws IOException {
         List<SerializationConfigurationType> listOfCapturedClasses = new ArrayList<>(serializations);
-        Collections.sort(listOfCapturedClasses);
-        printSerializationClasses(writer, listOfCapturedClasses);
+        JsonPrinter.printCollection(writer, listOfCapturedClasses, Comparator.naturalOrder(), SerializationConfigurationType::printJson);
     }
 
     @Override
     public void printLegacyJson(JsonWriter writer) throws IOException {
-        writer.append('{').indent().newline();
+        writer.appendObjectStart();
         List<SerializationConfigurationType> listOfCapturedClasses = new ArrayList<>(serializations);
-        Collections.sort(listOfCapturedClasses);
-        writer.quote("types").append(":");
-        printSerializationClasses(writer, listOfCapturedClasses);
-        writer.append(",").newline();
+        writer.quote("types").appendFieldSeparator();
+        JsonPrinter.printCollection(writer, listOfCapturedClasses, Comparator.naturalOrder(), SerializationConfigurationType::printLegacyJson);
+        writer.appendSeparator();
         List<SerializationConfigurationLambdaCapturingType> listOfCapturingClasses = new ArrayList<>(lambdaSerializationCapturingTypes);
-        listOfCapturingClasses.sort(new SerializationConfigurationLambdaCapturingType.SerializationConfigurationLambdaCapturingTypesComparator());
-        writer.quote("lambdaCapturingTypes").append(":");
-        printSerializationClasses(writer, listOfCapturingClasses);
-        writer.append(",").newline().quote("proxies").append(":");
+        writer.quote("lambdaCapturingTypes").appendFieldSeparator();
+        JsonPrinter.printCollection(writer, listOfCapturingClasses, Comparator.naturalOrder(), SerializationConfigurationLambdaCapturingType::printJson);
+        writer.appendSeparator().quote("proxies").appendFieldSeparator();
         printProxies(writer);
-        writer.unindent().newline();
-        writer.append('}');
+        writer.appendObjectEnd();
     }
 
     @Override
@@ -148,26 +144,6 @@ private void printProxies(JsonWriter writer) throws IOException {
         ProxyConfiguration.printProxyInterfaces(writer, lists);
     }
 
-    private static void printSerializationClasses(JsonWriter writer, List<? extends JsonPrintable> serializationConfigurationTypes) throws IOException {
-        writer.append('[');
-        writer.indent();
-
-        printSerializationTypes(serializationConfigurationTypes, writer);
-
-        writer.unindent().newline();
-        writer.append("]");
-    }
-
-    private static void printSerializationTypes(List<? extends JsonPrintable> serializationConfigurationTypes, JsonWriter writer) throws IOException {
-        String prefix = "";
-
-        for (JsonPrintable type : serializationConfigurationTypes) {
-            writer.append(prefix).newline();
-            type.printJson(writer);
-            prefix = ",";
-        }
-    }
-
     @Override
     public void registerIncludingAssociatedClasses(UnresolvedConfigurationCondition condition, Class<?> clazz) {
         register(condition, clazz);
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfigurationLambdaCapturingType.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfigurationLambdaCapturingType.java
index d8bb8e3912c2..0e7798618d1e 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfigurationLambdaCapturingType.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfigurationLambdaCapturingType.java
@@ -25,7 +25,6 @@
 package com.oracle.svm.configure.config;
 
 import java.io.IOException;
-import java.util.Comparator;
 import java.util.Objects;
 
 import org.graalvm.nativeimage.impl.UnresolvedConfigurationCondition;
@@ -35,7 +34,7 @@
 import jdk.graal.compiler.util.json.JsonPrintable;
 import jdk.graal.compiler.util.json.JsonWriter;
 
-public class SerializationConfigurationLambdaCapturingType implements JsonPrintable {
+public class SerializationConfigurationLambdaCapturingType implements JsonPrintable, Comparable<SerializationConfigurationLambdaCapturingType> {
     private final UnresolvedConfigurationCondition condition;
     private final String qualifiedJavaName;
 
@@ -82,15 +81,12 @@ public int hashCode() {
         return Objects.hash(condition, qualifiedJavaName);
     }
 
-    public static final class SerializationConfigurationLambdaCapturingTypesComparator implements Comparator<SerializationConfigurationLambdaCapturingType> {
-
-        @Override
-        public int compare(SerializationConfigurationLambdaCapturingType o1, SerializationConfigurationLambdaCapturingType o2) {
-            int compareName = o1.qualifiedJavaName.compareTo(o2.qualifiedJavaName);
-            if (compareName != 0) {
-                return compareName;
-            }
-            return o1.condition.compareTo(o2.condition);
+    @Override
+    public int compareTo(SerializationConfigurationLambdaCapturingType other) {
+        int compareName = qualifiedJavaName.compareTo(other.qualifiedJavaName);
+        if (compareName != 0) {
+            return compareName;
         }
+        return condition.compareTo(other.condition);
     }
 }
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfigurationType.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfigurationType.java
index d5531b26c13d..21a96a62368f 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfigurationType.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/config/SerializationConfigurationType.java
@@ -66,15 +66,23 @@ public UnresolvedConfigurationCondition getCondition() {
 
     @Override
     public void printJson(JsonWriter writer) throws IOException {
-        writer.append('{').indent().newline();
+        printJson(writer, SerializationConfigurationParser.TYPE_KEY);
+    }
+
+    public void printLegacyJson(JsonWriter writer) throws IOException {
+        printJson(writer, SerializationConfigurationParser.NAME_KEY);
+    }
+
+    private void printJson(JsonWriter writer, String key) throws IOException {
+        writer.appendObjectStart();
         ConfigurationConditionPrintable.printConditionAttribute(condition, writer);
-        writer.quote(SerializationConfigurationParser.TYPE_KEY).append(':').quote(qualifiedJavaName);
+        writer.quote(key).appendFieldSeparator().quote(qualifiedJavaName);
         if (qualifiedCustomTargetConstructorJavaName != null) {
-            writer.append(',').newline();
-            writer.quote(SerializationConfigurationParser.CUSTOM_TARGET_CONSTRUCTOR_CLASS_KEY).append(':')
+            writer.appendSeparator();
+            writer.quote(SerializationConfigurationParser.CUSTOM_TARGET_CONSTRUCTOR_CLASS_KEY).appendFieldSeparator()
                             .quote(qualifiedCustomTargetConstructorJavaName);
         }
-        writer.unindent().newline().append('}');
+        writer.appendObjectEnd();
     }
 
     @Override
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/AccessAdvisor.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/AccessAdvisor.java
index 31e5719d0ba0..c92f55613062 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/AccessAdvisor.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/AccessAdvisor.java
@@ -84,6 +84,7 @@ public final class AccessAdvisor {
         internalCallerFilter.addOrGetChildren("java.time.**", ConfigurationFilter.Inclusion.Exclude);
         internalCallerFilter.addOrGetChildren("java.util.**", ConfigurationFilter.Inclusion.Exclude);
         internalCallerFilter.addOrGetChildren("java.util.concurrent.atomic.*", ConfigurationFilter.Inclusion.Include); // Atomic*FieldUpdater
+        internalCallerFilter.addOrGetChildren("java.util.concurrent.atomic.AtomicReference", ConfigurationFilter.Inclusion.Exclude); // AtomicReference.<clinit>
         internalCallerFilter.addOrGetChildren("java.util.Collections", ConfigurationFilter.Inclusion.Include); // java.util.Collections.zeroLengthArray
         // LogRecord.readObject looks up resource bundles
         internalCallerFilter.addOrGetChildren("java.util.logging.LogRecord", ConfigurationFilter.Inclusion.Include);
@@ -212,30 +213,54 @@ public boolean shouldIgnore(LazyValue<String> queriedClass, LazyValue<String> ca
         return shouldIgnore(queriedClass, callerClass, true);
     }
 
-    public boolean shouldIgnoreJniMethodLookup(LazyValue<String> queriedClass, LazyValue<String> name, LazyValue<String> signature, LazyValue<String> callerClass) {
+    record JNICallDescriptor(String declaringClass, String name, String signature, boolean required) {
+        public boolean matches(String otherDeclaringClass, String otherName, String otherSignature) {
+            return (declaringClass == null || declaringClass.equals(otherDeclaringClass)) &&
+                            (otherName == null || name.equals(otherName)) &&
+                            (otherSignature == null || signature.equals(otherSignature));
+        }
+    }
+
+    private static final JNICallDescriptor[] JNI_STARTUP_SEQUENCE = new JNICallDescriptor[]{
+                    new JNICallDescriptor("sun.launcher.LauncherHelper", "getApplicationClass", "()Ljava/lang/Class;", true),
+                    new JNICallDescriptor("java.lang.Class", "getCanonicalName", "()Ljava/lang/String;", false),
+                    new JNICallDescriptor("java.lang.String", "lastIndexOf", "(I)I", false),
+                    new JNICallDescriptor("java.lang.String", "substring", "(I)Ljava/lang/String;", false),
+                    new JNICallDescriptor("java.lang.System", "getProperty", "(Ljava/lang/String;)Ljava/lang/String;", false),
+                    new JNICallDescriptor("java.lang.System", "setProperty", "(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;", false),
+                    new JNICallDescriptor(null, "main", "([Ljava/lang/String;)V", true),
+    };
+
+    public boolean shouldIgnoreJniLookup(LazyValue<String> queriedClass, LazyValue<String> name, LazyValue<String> signature, LazyValue<String> callerClass) {
         assert !shouldIgnore(queriedClass, callerClass) : "must have been checked before";
         if (!heuristicsEnabled) {
             return false;
         }
-        // Heuristic to ignore this sequence during startup:
-        // 1. Lookup of LauncherHelper.getApplicationClass()
-        // 2. Lookup of Class.getCanonicalName() -- only on Darwin
-        // 3. Lookup of application's main(String[])
-        if ("sun.launcher.LauncherHelper".equals(queriedClass.get())) {
-            if (launchPhase == 0 && "getApplicationClass".equals(name.get()) && "()Ljava/lang/Class;".equals(signature.get())) {
-                launchPhase = 1;
+        if (launchPhase >= 0) {
+            JNICallDescriptor expectedCall = JNI_STARTUP_SEQUENCE[launchPhase];
+            while (!expectedCall.matches(queriedClass.get(), name.get(), signature.get())) {
+                if ("sun.launcher.LauncherHelper".equals(queriedClass.get())) {
+                    return true;
+                }
+                if (!expectedCall.required) {
+                    launchPhase++;
+                    expectedCall = JNI_STARTUP_SEQUENCE[launchPhase];
+                } else {
+                    launchPhase = -1;
+                    return false;
+                }
             }
-            return true;
-        }
-        if (launchPhase == 1 && "getCanonicalName".equals(name.get()) && "()Ljava/lang/String;".equals(signature.get())) {
-            launchPhase = 2;
-            return true;
-        }
-        if (launchPhase > 0) {
-            launchPhase = -1;
-            if ("main".equals(name.get()) && "([Ljava/lang/String;)V".equals(signature.get())) {
-                return true;
+            if (name.get() != null && signature.get() != null) {
+                /*
+                 * We ignore class lookups before field/method lookups but don't skip to the next
+                 * query
+                 */
+                launchPhase++;
+            }
+            if (launchPhase == JNI_STARTUP_SEQUENCE.length) {
+                launchPhase = -1;
             }
+            return true;
         }
         /*
          * NOTE: JVM invocations cannot be reliably filtered with callerClass == null because these
@@ -245,6 +270,10 @@ public boolean shouldIgnoreJniMethodLookup(LazyValue<String> queriedClass, LazyV
         return false;
     }
 
+    public static boolean shouldIgnoreResourceLookup(LazyValue<String> resource) {
+        return resource.get().equals("META-INF/services/jdk.vm.ci.services.JVMCIServiceLocator");
+    }
+
     public boolean shouldIgnoreLoadClass(LazyValue<String> queriedClass, LazyValue<String> callerClass) {
         assert !shouldIgnore(queriedClass, callerClass) : "must have been checked before";
         if (!heuristicsEnabled) {
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/JniProcessor.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/JniProcessor.java
index f6fb770cd8f2..8c973e41fc6b 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/JniProcessor.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/JniProcessor.java
@@ -24,6 +24,7 @@
  */
 package com.oracle.svm.configure.trace;
 
+import static com.oracle.svm.configure.trace.LazyValueUtils.lazyNull;
 import static com.oracle.svm.configure.trace.LazyValueUtils.lazyValue;
 
 import java.util.List;
@@ -64,9 +65,12 @@ void processEntry(EconomicMap<String, ?> entry, ConfigurationSet configurationSe
             String lookupName = singleElement(args);
             String internalName = (lookupName.charAt(0) != '[') ? ('L' + lookupName + ';') : lookupName;
             String forNameString = MetaUtil.internalNameToJava(internalName, true, true);
-            if (!advisor.shouldIgnore(lazyValue(forNameString), callerClassLazyValue)) {
+            LazyValue<String> forNameStringLazyValue = lazyValue(forNameString);
+            if (!advisor.shouldIgnore(forNameStringLazyValue, callerClassLazyValue)) {
                 if (function.equals("FindClass")) {
-                    configurationSet.getJniConfiguration().getOrCreateType(condition, forNameString);
+                    if (!advisor.shouldIgnoreJniLookup(forNameStringLazyValue, lazyNull(), lazyNull(), callerClassLazyValue)) {
+                        configurationSet.getJniConfiguration().getOrCreateType(condition, forNameString);
+                    }
                 } else if (!AccessAdvisor.PROXY_CLASS_NAME_PATTERN.matcher(lookupName).matches()) { // DefineClass
                     LogUtils.warning("Unsupported JNI function DefineClass used to load class " + forNameString);
                 }
@@ -95,7 +99,7 @@ void processEntry(EconomicMap<String, ?> entry, ConfigurationSet configurationSe
                 expectSize(args, 2);
                 String name = (String) args.get(0);
                 String signature = (String) args.get(1);
-                if (!advisor.shouldIgnoreJniMethodLookup(lazyValue(clazz), lazyValue(name), lazyValue(signature), callerClassLazyValue)) {
+                if (!advisor.shouldIgnoreJniLookup(lazyValue(clazz), lazyValue(name), lazyValue(signature), callerClassLazyValue)) {
                     config.getOrCreateType(condition, declaringClassOrClazz).addMethod(name, signature, declaration);
                     if (!declaringClassOrClazz.equals(clazz)) {
                         config.getOrCreateType(condition, clazz);
@@ -107,9 +111,12 @@ void processEntry(EconomicMap<String, ?> entry, ConfigurationSet configurationSe
             case "GetStaticFieldID": {
                 expectSize(args, 2);
                 String name = (String) args.get(0);
-                config.getOrCreateType(condition, declaringClassOrClazz).addField(name, declaration, false);
-                if (!declaringClassOrClazz.equals(clazz)) {
-                    config.getOrCreateType(condition, clazz);
+                String signature = (String) args.get(1);
+                if (!advisor.shouldIgnoreJniLookup(lazyValue(clazz), lazyValue(name), lazyValue(signature), callerClassLazyValue)) {
+                    config.getOrCreateType(condition, declaringClassOrClazz).addField(name, declaration, false);
+                    if (!declaringClassOrClazz.equals(clazz)) {
+                        config.getOrCreateType(condition, clazz);
+                    }
                 }
                 break;
             }
@@ -117,7 +124,7 @@ void processEntry(EconomicMap<String, ?> entry, ConfigurationSet configurationSe
                 expectSize(args, 1); // exception message, ignore
                 String name = ConfigurationMethod.CONSTRUCTOR_NAME;
                 String signature = "(Ljava/lang/String;)V";
-                if (!advisor.shouldIgnoreJniMethodLookup(lazyValue(clazz), lazyValue(name), lazyValue(signature), callerClassLazyValue)) {
+                if (!advisor.shouldIgnoreJniLookup(lazyValue(clazz), lazyValue(name), lazyValue(signature), callerClassLazyValue)) {
                     config.getOrCreateType(condition, declaringClassOrClazz).addMethod(name, signature, declaration);
                     assert declaringClassOrClazz.equals(clazz) : "Constructor can only be accessed via declaring class";
                 }
diff --git a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/ReflectionProcessor.java b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/ReflectionProcessor.java
index e81dfdad9763..9788d607c0bc 100644
--- a/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/ReflectionProcessor.java
+++ b/substratevm/src/com.oracle.svm.configure/src/com/oracle/svm/configure/trace/ReflectionProcessor.java
@@ -37,6 +37,7 @@
 import com.oracle.svm.configure.config.ConfigurationMemberInfo.ConfigurationMemberDeclaration;
 import com.oracle.svm.configure.config.ConfigurationMethod;
 import com.oracle.svm.configure.config.ConfigurationSet;
+import com.oracle.svm.configure.config.ConfigurationType;
 import com.oracle.svm.configure.config.ResourceConfiguration;
 import com.oracle.svm.configure.config.SignatureUtil;
 import com.oracle.svm.configure.config.TypeConfiguration;
@@ -78,12 +79,16 @@ public void processEntry(EconomicMap<String, ?> entry, ConfigurationSet configur
                 expectSize(args, 2);
                 String module = (String) args.get(0);
                 String resource = (String) args.get(1);
-                resourceConfiguration.addGlobPattern(condition, resource, module);
+                if (!AccessAdvisor.shouldIgnoreResourceLookup(lazyValue(resource))) {
+                    resourceConfiguration.addGlobPattern(condition, resource, module);
+                }
                 return;
             }
             case "getResource", "getSystemResource", "getSystemResourceAsStream", "getResources", "getSystemResources" -> {
                 String literal = singleElement(args);
-                resourceConfiguration.addGlobPattern(condition, literal, null);
+                if (!AccessAdvisor.shouldIgnoreResourceLookup(lazyValue(literal))) {
+                    resourceConfiguration.addGlobPattern(condition, literal, null);
+                }
                 return;
             }
         }
@@ -203,8 +208,10 @@ public void processEntry(EconomicMap<String, ?> entry, ConfigurationSet configur
                 if (parameterTypes == null) { // tolerated and equivalent to no parameter types
                     parameterTypes = Collections.emptyList();
                 }
-                configuration.getOrCreateType(condition, clazzOrDeclaringClass).addMethod(name, SignatureUtil.toInternalSignature(parameterTypes), declaration, accessibility);
-                if (!clazzOrDeclaringClass.equals(clazz)) {
+                if (accessibility == ConfigurationMemberAccessibility.ACCESSED) {
+                    configuration.getOrCreateType(condition, clazzOrDeclaringClass).addMethod(name, SignatureUtil.toInternalSignature(parameterTypes), declaration, accessibility);
+                }
+                if (accessibility == ConfigurationMemberAccessibility.QUERIED || (!trackReflectionMetadata && !clazzOrDeclaringClass.equals(clazz))) {
                     configuration.getOrCreateType(condition, clazz);
                 }
                 break;
@@ -225,7 +232,10 @@ public void processEntry(EconomicMap<String, ?> entry, ConfigurationSet configur
                 }
                 String signature = SignatureUtil.toInternalSignature(parameterTypes);
                 assert clazz.equals(clazzOrDeclaringClass) : "Constructor can only be accessed via declaring class";
-                configuration.getOrCreateType(condition, clazzOrDeclaringClass).addMethod(ConfigurationMethod.CONSTRUCTOR_NAME, signature, declaration, accessibility);
+                ConfigurationType configurationType = configuration.getOrCreateType(condition, clazzOrDeclaringClass);
+                if (accessibility == ConfigurationMemberAccessibility.ACCESSED) {
+                    configurationType.addMethod(ConfigurationMethod.CONSTRUCTOR_NAME, signature, declaration, accessibility);
+                }
                 break;
             }
 
@@ -284,7 +294,7 @@ public void processEntry(EconomicMap<String, ?> entry, ConfigurationSet configur
     @SuppressWarnings("unchecked")
     private static ConfigurationTypeDescriptor descriptorForClass(Object clazz) {
         if (clazz instanceof List<?>) {
-            return new ProxyConfigurationTypeDescriptor(((List<String>) clazz).toArray(String[]::new));
+            return new ProxyConfigurationTypeDescriptor((List<String>) clazz);
         } else {
             return new NamedConfigurationTypeDescriptor((String) clazz);
         }
diff --git a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/ConfigurationParser.java b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/ConfigurationParser.java
index 93f4d559f21c..23730c8a4ca2 100644
--- a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/ConfigurationParser.java
+++ b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/ConfigurationParser.java
@@ -265,12 +265,9 @@ private static JsonParserException failOnSchemaError(String message) {
     protected record TypeDescriptorWithOrigin(ConfigurationTypeDescriptor typeDescriptor, boolean definedAsType) {
     }
 
-    protected static Optional<TypeDescriptorWithOrigin> parseTypeOrName(EconomicMap<String, Object> data, boolean treatAllNameEntriesAsType) {
-        Object typeObject = data.get(TYPE_KEY);
+    protected static Optional<TypeDescriptorWithOrigin> parseName(EconomicMap<String, Object> data, boolean treatAllNameEntriesAsType) {
         Object name = data.get(NAME_KEY);
-        if (typeObject != null) {
-            return parseTypeContents(typeObject).map(typeDescriptor -> new TypeDescriptorWithOrigin(typeDescriptor, true));
-        } else if (name != null) {
+        if (name != null) {
             NamedConfigurationTypeDescriptor typeDescriptor = new NamedConfigurationTypeDescriptor(asString(name));
             return Optional.of(new TypeDescriptorWithOrigin(typeDescriptor, treatAllNameEntriesAsType));
         } else {
@@ -298,7 +295,7 @@ protected static Optional<ConfigurationTypeDescriptor> parseTypeContents(Object
 
     private static ProxyConfigurationTypeDescriptor getProxyDescriptor(Object proxyObject) {
         List<Object> proxyInterfaces = asList(proxyObject, "proxy interface content should be an interface list");
-        String[] proxyInterfaceNames = proxyInterfaces.stream().map(obj -> asString(obj, "proxy")).toArray(String[]::new);
+        List<String> proxyInterfaceNames = proxyInterfaces.stream().map(obj -> asString(obj, "proxy")).toList();
         return new ProxyConfigurationTypeDescriptor(proxyInterfaceNames);
     }
 }
diff --git a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/LegacyReflectionConfigurationParser.java b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/LegacyReflectionConfigurationParser.java
index 6a7a40795332..a123418dc670 100644
--- a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/LegacyReflectionConfigurationParser.java
+++ b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/LegacyReflectionConfigurationParser.java
@@ -26,7 +26,6 @@
 
 import java.net.URI;
 import java.util.Arrays;
-import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
 
@@ -38,7 +37,7 @@
 
 final class LegacyReflectionConfigurationParser<C, T> extends ReflectionConfigurationParser<C, T> {
 
-    private static final List<String> OPTIONAL_REFLECT_CONFIG_OBJECT_ATTRS = Arrays.asList("name", "type", "allDeclaredConstructors", "allPublicConstructors",
+    private static final List<String> OPTIONAL_REFLECT_CONFIG_OBJECT_ATTRS = Arrays.asList("allDeclaredConstructors", "allPublicConstructors",
                     "allDeclaredMethods", "allPublicMethods", "allDeclaredFields", "allPublicFields",
                     "allDeclaredClasses", "allRecordComponents", "allPermittedSubclasses", "allNestMembers", "allSigners",
                     "allPublicClasses", "methods", "queriedMethods", "fields", CONDITIONAL_KEY,
@@ -59,10 +58,9 @@ public void parseAndRegister(Object json, URI origin) {
 
     @Override
     protected void parseClass(EconomicMap<String, Object> data) {
-        checkAttributes(data, "reflection class descriptor object", Collections.emptyList(), OPTIONAL_REFLECT_CONFIG_OBJECT_ATTRS);
-        checkHasExactlyOneAttribute(data, "reflection class descriptor object", List.of(NAME_KEY, TYPE_KEY));
+        checkAttributes(data, "reflection class descriptor object", List.of(NAME_KEY), OPTIONAL_REFLECT_CONFIG_OBJECT_ATTRS);
 
-        Optional<TypeDescriptorWithOrigin> type = parseTypeOrName(data, treatAllNameEntriesAsType);
+        Optional<TypeDescriptorWithOrigin> type = parseName(data, treatAllNameEntriesAsType);
         if (type.isEmpty()) {
             return;
         }
diff --git a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/LegacySerializationConfigurationParser.java b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/LegacySerializationConfigurationParser.java
index b03876c7ed44..46c92f8b389c 100644
--- a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/LegacySerializationConfigurationParser.java
+++ b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/LegacySerializationConfigurationParser.java
@@ -28,7 +28,6 @@
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
-import java.util.Optional;
 
 import org.graalvm.collections.EconomicMap;
 import org.graalvm.nativeimage.impl.RuntimeSerializationSupport;
@@ -85,18 +84,11 @@ protected void parseSerializationDescriptorObject(EconomicMap<String, Object> da
         if (lambdaCapturingType) {
             checkAttributes(data, "serialization descriptor object", Collections.singleton(NAME_KEY), Collections.singleton(CONDITIONAL_KEY));
         } else {
-            checkAttributes(data, "serialization descriptor object", Collections.emptySet(), Arrays.asList(TYPE_KEY, NAME_KEY, CUSTOM_TARGET_CONSTRUCTOR_CLASS_KEY, CONDITIONAL_KEY));
-            checkHasExactlyOneAttribute(data, "serialization descriptor object", List.of(TYPE_KEY, NAME_KEY));
+            checkAttributes(data, "serialization descriptor object", Collections.singleton(NAME_KEY), Arrays.asList(CUSTOM_TARGET_CONSTRUCTOR_CLASS_KEY, CONDITIONAL_KEY));
         }
 
-        Optional<TypeDescriptorWithOrigin> target = parseTypeOrName(data, false);
-        if (target.isEmpty()) {
-            return;
-        }
-        ConfigurationTypeDescriptor targetSerializationClass = target.get().typeDescriptor();
-        boolean definedAsType = target.get().definedAsType();
-
-        UnresolvedConfigurationCondition unresolvedCondition = parseCondition(data, definedAsType);
+        ConfigurationTypeDescriptor targetSerializationClass = new NamedConfigurationTypeDescriptor(asString(data.get(NAME_KEY)));
+        UnresolvedConfigurationCondition unresolvedCondition = parseCondition(data, false);
         var condition = conditionResolver.resolveCondition(unresolvedCondition);
         if (!condition.isPresent()) {
             return;
@@ -111,7 +103,7 @@ protected void parseSerializationDescriptorObject(EconomicMap<String, Object> da
             if (targetSerializationClass instanceof NamedConfigurationTypeDescriptor namedClass) {
                 serializationSupport.registerWithTargetConstructorClass(condition.get(), namedClass.name(), customTargetConstructorClass);
             } else if (targetSerializationClass instanceof ProxyConfigurationTypeDescriptor proxyClass) {
-                serializationSupport.registerProxyClass(condition.get(), Arrays.asList(proxyClass.interfaceNames()));
+                serializationSupport.registerProxyClass(condition.get(), proxyClass.interfaceNames());
             } else {
                 throw new JsonParserException("Unknown configuration type descriptor: %s".formatted(targetSerializationClass.toString()));
             }
diff --git a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/PredefinedClassesConfigurationParser.java b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/PredefinedClassesConfigurationParser.java
index f477fd180829..532db43ab1b5 100644
--- a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/PredefinedClassesConfigurationParser.java
+++ b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/PredefinedClassesConfigurationParser.java
@@ -29,11 +29,14 @@
 import java.io.InputStream;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.Collections;
 
 import org.graalvm.collections.EconomicMap;
 
+import jdk.graal.compiler.phases.common.LazyValue;
 import jdk.graal.compiler.util.json.JsonParserException;
 
 public class PredefinedClassesConfigurationParser extends ConfigurationParser {
@@ -121,4 +124,14 @@ private void parseClass(URI baseUri, EconomicMap<String, Object> data) {
         String nameInfo = asNullableString(data.get("nameInfo"), "nameInfo");
         registry.add(nameInfo, hash, baseUri);
     }
+
+    public static LazyValue<Path> directorySupplier(Path root) {
+        return new LazyValue<>(() -> {
+            try {
+                return Files.createDirectories(root.resolve(ConfigurationFile.PREDEFINED_CLASSES_AGENT_EXTRACTED_SUBDIR));
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
+        });
+    }
 }
diff --git a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/ProxyConfigurationTypeDescriptor.java b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/ProxyConfigurationTypeDescriptor.java
index 77b539e8a66a..c60f589852c9 100644
--- a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/ProxyConfigurationTypeDescriptor.java
+++ b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/ProxyConfigurationTypeDescriptor.java
@@ -28,17 +28,16 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
-import java.util.Set;
 
 import com.oracle.svm.core.reflect.proxy.DynamicProxySupport;
 
 import jdk.graal.compiler.util.json.JsonPrinter;
 import jdk.graal.compiler.util.json.JsonWriter;
 
-public record ProxyConfigurationTypeDescriptor(String[] interfaceNames) implements ConfigurationTypeDescriptor {
+public record ProxyConfigurationTypeDescriptor(List<String> interfaceNames) implements ConfigurationTypeDescriptor {
 
-    public ProxyConfigurationTypeDescriptor(String[] interfaceNames) {
-        this.interfaceNames = Arrays.stream(interfaceNames).map(ConfigurationTypeDescriptor::checkQualifiedJavaName).toArray(String[]::new);
+    public ProxyConfigurationTypeDescriptor(List<String> interfaceNames) {
+        this.interfaceNames = interfaceNames.stream().map(ConfigurationTypeDescriptor::checkQualifiedJavaName).toList();
     }
 
     @Override
@@ -48,18 +47,18 @@ public Kind getDescriptorType() {
 
     @Override
     public String toString() {
-        return DynamicProxySupport.proxyTypeDescriptor(interfaceNames);
+        return DynamicProxySupport.proxyTypeDescriptor(interfaceNames.toArray(String[]::new));
     }
 
     @Override
     public Collection<String> getAllQualifiedJavaNames() {
-        return Set.of(interfaceNames);
+        return interfaceNames;
     }
 
     @Override
     public int compareTo(ConfigurationTypeDescriptor other) {
         if (other instanceof ProxyConfigurationTypeDescriptor proxyOther) {
-            return Arrays.compare(interfaceNames, proxyOther.interfaceNames);
+            return Arrays.compare(interfaceNames.toArray(String[]::new), proxyOther.interfaceNames.toArray(String[]::new));
         } else {
             return getDescriptorType().compareTo(other.getDescriptorType());
         }
@@ -67,9 +66,9 @@ public int compareTo(ConfigurationTypeDescriptor other) {
 
     @Override
     public void printJson(JsonWriter writer) throws IOException {
-        writer.append("{").indent().newline();
-        writer.quote("proxy").append(":");
-        JsonPrinter.printCollection(writer, List.of(interfaceNames), null, (String p, JsonWriter w) -> w.quote(p));
-        writer.unindent().newline().append("}");
+        writer.appendObjectStart();
+        writer.quote("proxy").appendFieldSeparator();
+        JsonPrinter.printCollection(writer, interfaceNames, null, (String p, JsonWriter w) -> w.quote(p));
+        writer.appendObjectEnd();
     }
 }
diff --git a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/SerializationConfigurationParser.java b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/SerializationConfigurationParser.java
index 87570bd767c9..e34d651a3030 100644
--- a/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/SerializationConfigurationParser.java
+++ b/substratevm/src/com.oracle.svm.core/src/com/oracle/svm/core/configure/SerializationConfigurationParser.java
@@ -25,7 +25,6 @@
  */
 package com.oracle.svm.core.configure;
 
-import java.util.Arrays;
 import java.util.List;
 
 import org.graalvm.collections.EconomicMap;
@@ -68,7 +67,7 @@ protected void registerType(ConfigurationTypeDescriptor targetSerializationClass
         if (targetSerializationClass instanceof NamedConfigurationTypeDescriptor namedClass) {
             serializationSupport.registerWithTargetConstructorClass(condition, namedClass.name(), customTargetConstructorClass);
         } else if (targetSerializationClass instanceof ProxyConfigurationTypeDescriptor proxyClass) {
-            serializationSupport.registerProxyClass(condition, Arrays.asList(proxyClass.interfaceNames()));
+            serializationSupport.registerProxyClass(condition, proxyClass.interfaceNames());
         } else {
             throw new JsonParserException("Unknown configuration type descriptor: %s".formatted(targetSerializationClass.toString()));
         }
diff --git a/substratevm/src/com.oracle.svm.hosted/src/com/oracle/svm/hosted/config/RegistryAdapter.java b/substratevm/src/com.oracle.svm.hosted/src/com/oracle/svm/hosted/config/RegistryAdapter.java
index 51f5de9d428e..76ea23a764d6 100644
--- a/substratevm/src/com.oracle.svm.hosted/src/com/oracle/svm/hosted/config/RegistryAdapter.java
+++ b/substratevm/src/com.oracle.svm.hosted/src/com/oracle/svm/hosted/config/RegistryAdapter.java
@@ -30,7 +30,6 @@
 import java.lang.reflect.Method;
 import java.lang.reflect.Modifier;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 import org.graalvm.nativeimage.ImageSingletons;
@@ -114,7 +113,7 @@ private TypeResult<Class<?>> resolveNamedType(NamedConfigurationTypeDescriptor t
 
     private TypeResult<Class<?>> resolveProxyType(ProxyConfigurationTypeDescriptor typeDescriptor) {
         String typeName = typeDescriptor.toString();
-        List<TypeResult<Class<?>>> interfaceResults = Arrays.stream(typeDescriptor.interfaceNames()).map(name -> resolveNamedType(new NamedConfigurationTypeDescriptor(name), false)).toList();
+        List<TypeResult<Class<?>>> interfaceResults = typeDescriptor.interfaceNames().stream().map(name -> resolveNamedType(new NamedConfigurationTypeDescriptor(name), false)).toList();
         List<Class<?>> interfaces = new ArrayList<>();
         for (TypeResult<Class<?>> intf : interfaceResults) {
             if (!intf.isPresent()) {