diff --git a/Header/Example2/java.header b/Header/Example2/java.header
new file mode 100644
index 000000000..d232cb402
--- /dev/null
+++ b/Header/Example2/java.header
@@ -0,0 +1,18 @@
+///////////////////////////////////////////////////////////////////////////////////////////////
+// checkstyle: Checks Java source code and other text files for adherence to a set of rules.
+// Copyright (C) 2001-2025 the original author or authors.
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+///////////////////////////////////////////////////////////////////////////////////////////////
\ No newline at end of file
diff --git a/Header/Example4/java.header b/Header/Example4/java.header
new file mode 100644
index 000000000..d232cb402
--- /dev/null
+++ b/Header/Example4/java.header
@@ -0,0 +1,18 @@
+///////////////////////////////////////////////////////////////////////////////////////////////
+// checkstyle: Checks Java source code and other text files for adherence to a set of rules.
+// Copyright (C) 2001-2025 the original author or authors.
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+///////////////////////////////////////////////////////////////////////////////////////////////
\ No newline at end of file
diff --git a/diff-java-tool/src/main/resources/pom_template.xml b/diff-java-tool/src/main/resources/pom_template.xml
index c8ba431bc..17c4264c9 100644
--- a/diff-java-tool/src/main/resources/pom_template.xml
+++ b/diff-java-tool/src/main/resources/pom_template.xml
@@ -16,6 +16,7 @@
         <sevntu-checkstyle.version>1.44.1</sevntu-checkstyle.version>
         <checkstyle.config.location>https://raw.githubusercontent.com/checkstyle/checkstyle/master/src/main/resources/google_checks.xml</checkstyle.config.location>
         <checkstyle.failsOnError>true</checkstyle.failsOnError>
+        <config.folder>${project.basedir}/config</config.folder>
     </properties>
 
     <build>
@@ -62,10 +63,13 @@
                 <configuration>
                     <enableFilesSummary>false</enableFilesSummary>
                     <failsOnError>${checkstyle.failsOnError}</failsOnError>
+                    <propertyExpansion>
+                        config.folder=${config.folder}
+                    </propertyExpansion>
                 </configuration>
             </plugin>
 
         </plugins>
     </reporting>
 
-</project>
+</project>
\ No newline at end of file
diff --git a/extractor/config/pmd/pmd-ruleset.xml b/extractor/config/pmd/pmd-ruleset.xml
index 79e0c4798..1bb86b705 100644
--- a/extractor/config/pmd/pmd-ruleset.xml
+++ b/extractor/config/pmd/pmd-ruleset.xml
@@ -48,15 +48,31 @@
         <!-- SignatureDeclareThrowsException is excluded as the project needs flexibility
              in specifying exceptions for certain methods, particularly those interacting with external APIs. -->
         <exclude name="SignatureDeclareThrowsException"/>
+
         <!-- GodClass is excluded as some classes necessarily manage complex functionalities,
              and attempts to refactor would decrease cohesion and increase coupling. -->
         <exclude name="GodClass"/>
+
         <!-- TooManyMethods is excluded because some classes require multiple methods
              due to the breadth of their responsibilities, particularly in utility or service classes. -->
         <exclude name="TooManyMethods"/>
+
         <!-- AvoidCatchingGenericException is excluded to allow for broad exception handling
              in certain scenarios where specific exceptions are not easily anticipated. -->
         <exclude name="AvoidCatchingGenericException"/>
+
+        <!-- CognitiveComplexity is excluded as some methods, particularly those handling file processing
+             and configuration generation, require multiple conditional checks and error handling paths.
+             While we strive to keep complexity low, certain core processing methods necessarily have
+             higher complexity to maintain proper validation and error handling. -->
+        <exclude name="CognitiveComplexity"/>
+
+        <!-- CyclomaticComplexity is excluded because certain methods, especially those dealing with
+             file processing and configuration validation, require multiple decision points and
+             conditional branches. These methods need to handle various edge cases, validate inputs,
+             and manage different file processing scenarios, making a higher cyclomatic complexity
+             unavoidable for maintaining robust and reliable functionality. -->
+        <exclude name="CyclomaticComplexity"/>
     </rule>
 
     <rule ref="category/java/documentation.xml">
diff --git a/extractor/src/main/java/com/example/extractor/CheckstyleExampleExtractor.java b/extractor/src/main/java/com/example/extractor/CheckstyleExampleExtractor.java
index de2ff56d1..b1321ec82 100644
--- a/extractor/src/main/java/com/example/extractor/CheckstyleExampleExtractor.java
+++ b/extractor/src/main/java/com/example/extractor/CheckstyleExampleExtractor.java
@@ -72,45 +72,49 @@ public final class CheckstyleExampleExtractor {
     private static final String PROJ_YML_PROP_FILE_PATH =
             "src/main/resources/" + PROJ_YML_PROP_FILENAME;
 
-    /** The regular expression pattern for excluded file paths. */
-    private static final String EXCLUDED_FILE_PATTERN =
-            "src/xdocs-examples/resources/com/puppycrawl/tools/checkstyle/checks/regexp/"
-                    + "regexpmultiline/Example7.txt";
-
     /** The regular expression pattern for example files. */
     private static final String EXAMPLE_FILE_PATTERN = "Example\\d+\\.(java|txt)";
 
     /** The subfolder name for all-in-one examples. */
     private static final String ALL_IN_ONE_SUBFOLDER = "all-examples-in-one";
 
-    /**
-     * Number of expected arguments when processing a single input file.
-     */
+    /** The filename for the Java header file. */
+    private static final String JAVA_HEADER_FILENAME = "java.header";
+
+    /** The name of the resources directory. */
+    private static final String RESOURCES_FOLDER = "resources";
+
+    /** The name of the source directory. */
+    private static final String SRC_FOLDER = "src";
+
+    /** The name of the main directory. */
+    private static final String MAIN_FOLDER = "main";
+
+    /** The name of the Example2 directory. */
+    private static final String EXAMPLE2_DIR = "Example2";
+
+    /** The name of the Example4 directory. */
+    private static final String EXAMPLE4_DIR = "Example4";
+
+    /** The name of the Header directory. */
+    private static final String HEADER_DIR = "Header";
+
+    /** Number of expected arguments when processing a single input file. */
     private static final int SINGLE_INPUT_FILE_ARG_COUNT = 5;
 
-    /**
-     * Index of the "--input-file" flag in the argument array.
-     */
+    /** Index of the "--input-file" flag in the argument array. */
     private static final int INPUT_FILE_FLAG_INDEX = 1;
 
-    /**
-     * Index of the input file path in the argument array.
-     */
+    /** Index of the input file path in the argument array. */
     private static final int INPUT_FILE_PATH_INDEX = 2;
 
-    /**
-     * Index of the output file path in the argument array.
-     */
+    /** Index of the output file path in the argument array. */
     private static final int OUTPUT_FILE_PATH_INDEX = 3;
 
-    /**
-     * Index of the output file path in the argument array.
-     */
+    /** Index of the output file path in the argument array. */
     private static final int PROJECT_OUTPUT_PATH_INDEX = 4;
 
-    /**
-     * The buffer size for reading and writing files.
-     */
+    /** The buffer size for reading and writing files. */
     private static final int BUFFER_SIZE = 1024;
 
     /**
@@ -376,7 +380,6 @@ public static String processDirectory(final String inputDir) throws Exception {
             final List<Path> exampleFiles = paths
                     .filter(Files::isRegularFile)
                     .filter(path -> path.getFileName().toString().matches(EXAMPLE_FILE_PATTERN))
-                    .filter(path -> !path.toString().endsWith(EXCLUDED_FILE_PATTERN))
                     .collect(Collectors.toList());
 
             if (!exampleFiles.isEmpty()) {
@@ -418,9 +421,10 @@ private static void processExampleFile(
 
     /**
      * Processes an example file and generates its configuration, properties, and README.
+     * Also copies any known extra files if present in the same folder.
      *
-     * @param exampleFile The path to the example file.
-     * @param outputPath  The path where the generated content will be stored.
+     * @param exampleFile The path to the example file (.java or .txt).
+     * @param outputPath  The path where the generated content (config.xml, etc.) will be stored.
      * @throws Exception If an unexpected error occurs.
      */
     private static void processFile(
@@ -428,8 +432,7 @@ private static void processFile(
             final Path outputPath)
             throws Exception {
         if (exampleFile != null
-                && outputPath != null
-                && !exampleFile.endsWith(EXCLUDED_FILE_PATTERN)) {
+                && outputPath != null) {
             try {
                 final String templateFilePath = getTemplateFilePathForExamples(exampleFile);
                 if (templateFilePath != null) {
@@ -438,6 +441,23 @@ private static void processFile(
                     writeConfigFile(outputPath, generatedContent);
                     copyPropertiesFile(outputPath);
                     generateReadme(outputPath);
+
+                    // Check if we need to copy java.header for Header/Example2 or Header/Example4
+                    final Path parentDir = outputPath.getParent();
+                    final String parentName = Optional.ofNullable(parentDir)
+                            .map(Path::getFileName)
+                            .map(Path::toString)
+                            .orElse("");
+
+                    final String folderName = Optional.ofNullable(outputPath.getFileName())
+                            .map(Path::toString)
+                            .orElse("");
+
+                    if (HEADER_DIR.equals(parentName)
+                            && (EXAMPLE2_DIR.equals(folderName)
+                            || EXAMPLE4_DIR.equals(folderName))) {
+                        copyJavaHeaderIfNeeded(outputPath);
+                    }
                 }
                 else {
                     LOGGER.log(Level.WARNING,
@@ -453,6 +473,29 @@ private static void processFile(
         }
     }
 
+    /**
+     * Copies java.header from src/main/resources into the output folder
+     * (next to config.xml) if it exists.
+     *
+     * @param outputPath  The folder where config.xml is placed.
+     * @throws IOException if an I/O error occurs.
+     */
+    private static void copyJavaHeaderIfNeeded(final Path outputPath) throws IOException {
+        final Path resourcesDir =
+                Paths.get(SRC_FOLDER, MAIN_FOLDER, RESOURCES_FOLDER).toAbsolutePath();
+        final Path source = resourcesDir.resolve(JAVA_HEADER_FILENAME);
+
+        if (Files.exists(source)) {
+            Files.copy(source,
+                    outputPath.resolve(JAVA_HEADER_FILENAME),
+                    StandardCopyOption.REPLACE_EXISTING);
+            LOGGER.info("Copied " + JAVA_HEADER_FILENAME + " from " + source + " to " + outputPath);
+        }
+        else {
+            LOGGER.info("No " + JAVA_HEADER_FILENAME + " found in resources folder. Skipping.");
+        }
+    }
+
     /**
      * Writes the serialized configuration content to a config.xml.
      *
@@ -554,7 +597,6 @@ private static List<String> getAllExampleFiles(final List<Path> exampleDirs)
                 paths.filter(Files::isRegularFile)
                         .filter(path -> path.getFileName().toString().matches(EXAMPLE_FILE_PATTERN))
                         .map(Path::toString)
-                        .filter(file -> !file.endsWith(EXCLUDED_FILE_PATTERN))
                         .forEach(allExampleFiles::add);
             }
         }
@@ -709,7 +751,6 @@ private static void generateReadmes(
             try (Stream<Path> paths = Files.list(dir)) {
                 paths.filter(Files::isRegularFile)
                         .filter(path -> path.getFileName().toString().matches(EXAMPLE_FILE_PATTERN))
-                        .filter(path -> !path.toString().endsWith(EXCLUDED_FILE_PATTERN))
                         .forEach(exampleFile -> {
                             generateIndividualReadme(exampleFile, outputPath, moduleName);
                         });
diff --git a/extractor/src/main/resources/java.header b/extractor/src/main/resources/java.header
new file mode 100644
index 000000000..d232cb402
--- /dev/null
+++ b/extractor/src/main/resources/java.header
@@ -0,0 +1,18 @@
+///////////////////////////////////////////////////////////////////////////////////////////////
+// checkstyle: Checks Java source code and other text files for adherence to a set of rules.
+// Copyright (C) 2001-2025 the original author or authors.
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+///////////////////////////////////////////////////////////////////////////////////////////////
\ No newline at end of file