diff --git a/build.gradle b/build.gradle
index e803b512..06db8ab3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -8,7 +8,7 @@ plugins {
 }
 
 group = 'stirling.software'
-version = '0.14.2'
+version = '0.14.3'
 sourceCompatibility = '17'
 
 repositories {
diff --git a/src/main/java/stirling/software/SPDF/config/ConfigInitializer.java b/src/main/java/stirling/software/SPDF/config/ConfigInitializer.java
index 9760662a..862f5718 100644
--- a/src/main/java/stirling/software/SPDF/config/ConfigInitializer.java
+++ b/src/main/java/stirling/software/SPDF/config/ConfigInitializer.java
@@ -12,6 +12,8 @@ import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
+import java.util.Set;
+import java.util.function.Function;
 import java.util.stream.Collectors;
 
 import org.springframework.context.ApplicationContextInitializer;
@@ -19,83 +21,109 @@ import org.springframework.context.ConfigurableApplicationContext;
 
 public class ConfigInitializer implements ApplicationContextInitializer<ConfigurableApplicationContext> {
 
-    @Override
-    public void initialize(ConfigurableApplicationContext applicationContext) {
-        try {
-            ensureConfigExists();
-        } catch (IOException e) {
-            throw new RuntimeException("Failed to initialize application configuration", e);
-        }
-    }
+	@Override
+	public void initialize(ConfigurableApplicationContext applicationContext) {
+		try {
+			ensureConfigExists();
+		} catch (IOException e) {
+			throw new RuntimeException("Failed to initialize application configuration", e);
+		}
+	}
 
-    public void ensureConfigExists() throws IOException {
-        // Define the path to the external config directory
-        Path destPath = Paths.get("configs", "settings.yml");
+	public void ensureConfigExists() throws IOException {
+		// Define the path to the external config directory
+		Path destPath = Paths.get("configs", "settings.yml");
 
-        // Check if the file already exists
-        if (Files.notExists(destPath)) {
-            // Ensure the destination directory exists
-            Files.createDirectories(destPath.getParent());
+		// Check if the file already exists
+		if (Files.notExists(destPath)) {
+			// Ensure the destination directory exists
+			Files.createDirectories(destPath.getParent());
 
-            // Copy the resource from classpath to the external directory
-            try (InputStream in = getClass().getClassLoader().getResourceAsStream("settings.yml.template")) {
-                if (in != null) {
-                    Files.copy(in, destPath);
-                } else {
-                    throw new FileNotFoundException("Resource file not found: settings.yml.template");
-                }
-            }
-        } else {
-            // If user file exists, we need to merge it with the template from the classpath
-            List<String> templateLines;
-            try (InputStream in = getClass().getClassLoader().getResourceAsStream("settings.yml.template")) {
-                templateLines = new BufferedReader(new InputStreamReader(in, StandardCharsets.UTF_8)).lines().collect(Collectors.toList());
-            }
+			// Copy the resource from classpath to the external directory
+			try (InputStream in = getClass().getClassLoader().getResourceAsStream("settings.yml.template")) {
+				if (in != null) {
+					Files.copy(in, destPath);
+				} else {
+					throw new FileNotFoundException("Resource file not found: settings.yml.template");
+				}
+			}
+		} else {
+			// If user file exists, we need to merge it with the template from the classpath
+			List<String> templateLines;
+			try (InputStream in = getClass().getClassLoader().getResourceAsStream("settings.yml.template")) {
+				templateLines = new BufferedReader(new InputStreamReader(in, StandardCharsets.UTF_8)).lines()
+						.collect(Collectors.toList());
+			}
 
-            mergeYamlFiles(templateLines, destPath, destPath);
-        }
-    }
+			mergeYamlFiles(templateLines, destPath, destPath);
+		}
+	}
 
-    public void mergeYamlFiles(List<String> templateLines, Path userFilePath, Path outputPath) throws IOException {
-        List<String> userLines = Files.readAllLines(userFilePath);
+	public void mergeYamlFiles(List<String> templateLines, Path userFilePath, Path outputPath) throws IOException {
+		List<String> userLines = Files.readAllLines(userFilePath);
+		List<String> mergedLines = new ArrayList<>();
+		boolean insideAutoGenerated = false;
+		boolean beforeFirstKey = true;
 
-        List<String> mergedLines = new ArrayList<>();
-        boolean insideAutoGenerated = false;
+		Function<String, Boolean> isCommented = line -> line.trim().startsWith("#");
+		Function<String, String> extractKey = line -> {
+			String[] parts = line.split(":");
+			return parts.length > 0 ? parts[0].trim().replace("#", "").trim() : "";
+		};
 
-        for (String line : templateLines) {
-            // Check if we've entered or left the AutomaticallyGenerated section
-            if (line.trim().equalsIgnoreCase("AutomaticallyGenerated:")) {
-                insideAutoGenerated = true;
-                mergedLines.add(line);
-                continue;
-            } else if (insideAutoGenerated && line.trim().isEmpty()) {
-                // We have reached the end of the AutomaticallyGenerated section
-                insideAutoGenerated = false;
-                mergedLines.add(line);
-                continue;
-            }
+		Set<String> userKeys = userLines.stream().map(extractKey).collect(Collectors.toSet());
 
-            if (insideAutoGenerated) {
-                // Add lines from user's settings if we are inside AutomaticallyGenerated
-                Optional<String> userAutoGenValue = userLines.stream().filter(l -> l.trim().startsWith(line.split(":")[0].trim())).findFirst();
-                if (userAutoGenValue.isPresent()) {
-                    mergedLines.add(userAutoGenValue.get());
-                    continue;
-                }
-            } else {
-                // Outside of AutomaticallyGenerated, continue as before
-                if (line.contains(": ")) {
-                    String key = line.split(": ")[0].trim();
-                    Optional<String> userValue = userLines.stream().filter(l -> l.trim().startsWith(key)).findFirst();
-                    if (userValue.isPresent()) {
-                        mergedLines.add(userValue.get());
-                        continue;
-                    }
-                }
-                mergedLines.add(line);
-            }
-        }
+		for (String line : templateLines) {
+			String key = extractKey.apply(line);
+
+			if (line.trim().equalsIgnoreCase("AutomaticallyGenerated:")) {
+				insideAutoGenerated = true;
+				mergedLines.add(line);
+				continue;
+			} else if (insideAutoGenerated && line.trim().isEmpty()) {
+				insideAutoGenerated = false;
+				mergedLines.add(line);
+				continue;
+			}
+
+			if (beforeFirstKey && (isCommented.apply(line) || line.trim().isEmpty())) {
+				// Handle top comments and empty lines before the first key.
+				mergedLines.add(line);
+				continue;
+			}
+
+			if (!key.isEmpty())
+				beforeFirstKey = false;
+
+			if (userKeys.contains(key)) {
+				// If user has any version (commented or uncommented) of this key, skip the
+				// template line
+				Optional<String> userValue = userLines.stream()
+						.filter(l -> extractKey.apply(l).equalsIgnoreCase(key) && !isCommented.apply(l)).findFirst();
+				if (userValue.isPresent())
+					mergedLines.add(userValue.get());
+				continue;
+			}
+
+			if (isCommented.apply(line) || line.trim().isEmpty() || !userKeys.contains(key)) {
+				mergedLines.add(line); // If line is commented, empty or key not present in user's file, retain the
+										// template line
+				continue;
+			}
+		}
+
+		// Add any additional uncommented user lines that are not present in the
+		// template
+		for (String userLine : userLines) {
+			String userKey = extractKey.apply(userLine);
+			boolean isPresentInTemplate = templateLines.stream().map(extractKey)
+					.anyMatch(templateKey -> templateKey.equalsIgnoreCase(userKey));
+			if (!isPresentInTemplate && !isCommented.apply(userLine)) {
+				mergedLines.add(userLine);
+			}
+		}
+
+		Files.write(outputPath, mergedLines, StandardCharsets.UTF_8);
+	}
 
-        Files.write(outputPath, mergedLines, StandardCharsets.UTF_8);
-    }
 }
\ No newline at end of file