diff --git a/jadx-cli/src/main/java/jadx/cli/JCommanderWrapper.java b/jadx-cli/src/main/java/jadx/cli/JCommanderWrapper.java
index 04114f5d1..58c50d093 100644
--- a/jadx-cli/src/main/java/jadx/cli/JCommanderWrapper.java
+++ b/jadx-cli/src/main/java/jadx/cli/JCommanderWrapper.java
@@ -27,7 +27,7 @@ import jadx.core.plugins.PluginContext;
 import jadx.core.utils.Utils;
 import jadx.plugins.tools.JadxExternalPluginsLoader;
 
-public class JCommanderWrapper<T> {
+public class JCommanderWrapper {
 	private final JCommander jc;
 	private final JadxCLIArgs argsObj;
 
@@ -42,6 +42,7 @@ public class JCommanderWrapper<T> {
 	public boolean parse(String[] args) {
 		try {
 			jc.parse(args);
+			applyFiles(argsObj);
 			return true;
 		} catch (ParameterException e) {
 			System.err.println("Arguments parse error: " + e.getMessage());
@@ -50,6 +51,15 @@ public class JCommanderWrapper<T> {
 		}
 	}
 
+	public void overrideProvided(JadxCLIArgs obj) {
+		applyFiles(obj);
+		for (ParameterDescription parameter : jc.getParameters()) {
+			if (parameter.isAssigned()) {
+				overrideProperty(obj, parameter);
+			}
+		}
+	}
+
 	public boolean processCommands() {
 		String parsedCommand = jc.getParsedCommand();
 		if (parsedCommand == null) {
@@ -58,20 +68,21 @@ public class JCommanderWrapper<T> {
 		return JadxCLICommands.process(this, jc, parsedCommand);
 	}
 
-	public void overrideProvided(JadxCLIArgs obj) {
-		List<ParameterDescription> fieldsParams = jc.getParameters();
-		List<ParameterDescription> parameters = new ArrayList<>(1 + fieldsParams.size());
-		parameters.add(jc.getMainParameterValue());
-		parameters.addAll(fieldsParams);
-		for (ParameterDescription parameter : parameters) {
-			if (parameter.isAssigned()) {
-				// copy assigned field value to obj
-				Parameterized parameterized = parameter.getParameterized();
-				Object providedValue = parameterized.get(parameter.getObject());
-				Object newValue = mergeValues(parameterized.getType(), providedValue, () -> parameterized.get(obj));
-				parameterized.set(obj, newValue);
-			}
-		}
+	/**
+	 * The main parameter parsing doesn't work if accepting unknown options
+	 */
+	private void applyFiles(JadxCLIArgs argsObj) {
+		argsObj.setFiles(jc.getUnknownOptions());
+	}
+
+	/**
+	 * Override assigned field value to obj
+	 */
+	private static void overrideProperty(JadxCLIArgs obj, ParameterDescription parameter) {
+		Parameterized parameterized = parameter.getParameterized();
+		Object providedValue = parameterized.get(parameter.getObject());
+		Object newValue = mergeValues(parameterized.getType(), providedValue, () -> parameterized.get(obj));
+		parameterized.set(obj, newValue);
 	}
 
 	@SuppressWarnings({ "rawtypes", "unchecked" })
@@ -85,10 +96,6 @@ public class JCommanderWrapper<T> {
 		return value;
 	}
 
-	public List<String> getUnknownOptions() {
-		return jc.getUnknownOptions();
-	}
-
 	public void printUsage() {
 		LogHelper.setLogLevel(LogHelper.LogLevelEnum.ERROR); // mute logger while printing help
 
diff --git a/jadx-cli/src/main/java/jadx/cli/JadxCLIArgs.java b/jadx-cli/src/main/java/jadx/cli/JadxCLIArgs.java
index b08e1f71b..e1bc03a1e 100644
--- a/jadx-cli/src/main/java/jadx/cli/JadxCLIArgs.java
+++ b/jadx-cli/src/main/java/jadx/cli/JadxCLIArgs.java
@@ -1,7 +1,6 @@
 package jadx.cli;
 
 import java.nio.file.Path;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.EnumSet;
 import java.util.HashMap;
@@ -36,7 +35,7 @@ import jadx.core.utils.files.FileUtils;
 public class JadxCLIArgs {
 
 	@Parameter(description = "<input files> (.apk, .dex, .jar, .class, .smali, .zip, .aar, .arsc, .aab, .xapk, .apkm, .jadx.kts)")
-	protected List<String> files = new ArrayList<>(1);
+	protected List<String> files;
 
 	@Parameter(names = { "-d", "--output-dir" }, description = "output directory")
 	protected String outDir;
@@ -283,29 +282,11 @@ public class JadxCLIArgs {
 	protected Map<String, String> pluginOptions = new HashMap<>();
 
 	public boolean processArgs(String[] args) {
-		JCommanderWrapper<JadxCLIArgs> jcw = new JCommanderWrapper<>(this);
+		JCommanderWrapper jcw = new JCommanderWrapper(this);
 		return jcw.parse(args) && process(jcw);
 	}
 
-	/**
-	 * Set values only for options provided in cmd.
-	 * Used to merge saved options and options passed in command line.
-	 */
-	public boolean overrideProvided(String[] args) {
-		JCommanderWrapper<JadxCLIArgs> jcw = new JCommanderWrapper<>(newInstance());
-		if (!jcw.parse(args)) {
-			return false;
-		}
-		jcw.overrideProvided(this);
-		return process(jcw);
-	}
-
-	protected JadxCLIArgs newInstance() {
-		return new JadxCLIArgs();
-	}
-
-	private boolean process(JCommanderWrapper<JadxCLIArgs> jcw) {
-		files.addAll(jcw.getUnknownOptions());
+	public boolean process(JCommanderWrapper jcw) {
 		if (jcw.processCommands()) {
 			return false;
 		}
@@ -388,6 +369,10 @@ public class JadxCLIArgs {
 		return files;
 	}
 
+	public void setFiles(List<String> files) {
+		this.files = files;
+	}
+
 	public String getOutDir() {
 		return outDir;
 	}
diff --git a/jadx-cli/src/main/java/jadx/cli/JadxCLICommands.java b/jadx-cli/src/main/java/jadx/cli/JadxCLICommands.java
index fface7016..210fd8bc8 100644
--- a/jadx-cli/src/main/java/jadx/cli/JadxCLICommands.java
+++ b/jadx-cli/src/main/java/jadx/cli/JadxCLICommands.java
@@ -24,7 +24,7 @@ public class JadxCLICommands {
 		COMMANDS_MAP.forEach(builder::addCommand);
 	}
 
-	public static boolean process(JCommanderWrapper<?> jcw, JCommander jc, String parsedCommand) {
+	public static boolean process(JCommanderWrapper jcw, JCommander jc, String parsedCommand) {
 		ICommand command = COMMANDS_MAP.get(parsedCommand);
 		if (command == null) {
 			throw new JadxArgsValidateException("Unknown command: " + parsedCommand
diff --git a/jadx-cli/src/main/java/jadx/cli/commands/CommandPlugins.java b/jadx-cli/src/main/java/jadx/cli/commands/CommandPlugins.java
index f388579c8..33d7d37d0 100644
--- a/jadx-cli/src/main/java/jadx/cli/commands/CommandPlugins.java
+++ b/jadx-cli/src/main/java/jadx/cli/commands/CommandPlugins.java
@@ -65,7 +65,7 @@ public class CommandPlugins implements ICommand {
 
 	@SuppressWarnings("UnnecessaryReturnStatement")
 	@Override
-	public void process(JCommanderWrapper<?> jcw, JCommander subCommander) {
+	public void process(JCommanderWrapper jcw, JCommander subCommander) {
 		if (printHelp) {
 			jcw.printUsage(subCommander);
 			return;
diff --git a/jadx-cli/src/main/java/jadx/cli/commands/ICommand.java b/jadx-cli/src/main/java/jadx/cli/commands/ICommand.java
index 3cfd0f273..0c8a3392c 100644
--- a/jadx-cli/src/main/java/jadx/cli/commands/ICommand.java
+++ b/jadx-cli/src/main/java/jadx/cli/commands/ICommand.java
@@ -7,5 +7,5 @@ import jadx.cli.JCommanderWrapper;
 public interface ICommand {
 	String name();
 
-	void process(JCommanderWrapper<?> jcw, JCommander subCommander);
+	void process(JCommanderWrapper jcw, JCommander subCommander);
 }
diff --git a/jadx-cli/src/test/java/jadx/cli/JadxCLIArgsTest.java b/jadx-cli/src/test/java/jadx/cli/JadxCLIArgsTest.java
index 8de22c50d..120947790 100644
--- a/jadx-cli/src/test/java/jadx/cli/JadxCLIArgsTest.java
+++ b/jadx-cli/src/test/java/jadx/cli/JadxCLIArgsTest.java
@@ -93,7 +93,16 @@ public class JadxCLIArgsTest {
 	}
 
 	private JadxCLIArgs override(JadxCLIArgs jadxArgs, String... args) {
-		return check(jadxArgs, jadxArgs.overrideProvided(args));
+		return check(jadxArgs, overrideProvided(jadxArgs, args));
+	}
+
+	private static boolean overrideProvided(JadxCLIArgs jadxArgs, String[] args) {
+		JCommanderWrapper jcw = new JCommanderWrapper(new JadxCLIArgs());
+		if (!jcw.parse(args)) {
+			return false;
+		}
+		jcw.overrideProvided(jadxArgs);
+		return jadxArgs.process(jcw);
 	}
 
 	private static JadxCLIArgs check(JadxCLIArgs jadxArgs, boolean res) {
diff --git a/jadx-commons/jadx-app-commons/src/main/java/jadx/commons/app/JadxCommonFiles.java b/jadx-commons/jadx-app-commons/src/main/java/jadx/commons/app/JadxCommonFiles.java
index 6ef21d44e..d49c37c5a 100644
--- a/jadx-commons/jadx-app-commons/src/main/java/jadx/commons/app/JadxCommonFiles.java
+++ b/jadx-commons/jadx-app-commons/src/main/java/jadx/commons/app/JadxCommonFiles.java
@@ -6,6 +6,8 @@ import java.nio.file.Path;
 import java.util.function.Function;
 
 import org.jetbrains.annotations.Nullable;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import dev.dirs.ProjectDirectories;
 import dev.dirs.impl.Windows;
@@ -13,6 +15,7 @@ import dev.dirs.impl.WindowsPowerShell;
 import dev.dirs.jni.WindowsJni;
 
 public class JadxCommonFiles {
+	private static final Logger LOG = LoggerFactory.getLogger(JadxCommonFiles.class);
 
 	private static final Path CONFIG_DIR;
 	private static final Path CACHE_DIR;
@@ -60,10 +63,21 @@ public class JadxCommonFiles {
 		}
 
 		private synchronized ProjectDirectories loadDirs() {
-			if (dirs == null) {
-				dirs = ProjectDirectories.from("io.github", "skylot", "jadx", DirsLoader::getWinDirs);
+			ProjectDirectories currentDirs = dirs;
+			if (currentDirs != null) {
+				return currentDirs;
 			}
-			return dirs;
+			LOG.debug("Loading system dirs ...");
+			long start = System.currentTimeMillis();
+
+			ProjectDirectories loadedDirs = ProjectDirectories.from("io.github", "skylot", "jadx", DirsLoader::getWinDirs);
+
+			if (LOG.isDebugEnabled()) {
+				LOG.debug("Loaded system dirs ({}ms): config: {}, cache: {}",
+						System.currentTimeMillis() - start, loadedDirs.configDir, loadedDirs.cacheDir);
+			}
+			dirs = loadedDirs;
+			return loadedDirs;
 		}
 
 		/**
diff --git a/jadx-gui/src/main/java/jadx/gui/JadxGUI.java b/jadx-gui/src/main/java/jadx/gui/JadxGUI.java
index bb702cd63..421fe605f 100644
--- a/jadx-gui/src/main/java/jadx/gui/JadxGUI.java
+++ b/jadx-gui/src/main/java/jadx/gui/JadxGUI.java
@@ -7,6 +7,7 @@ import javax.swing.SwingUtilities;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import jadx.cli.JCommanderWrapper;
 import jadx.cli.LogHelper;
 import jadx.core.utils.files.FileUtils;
 import jadx.gui.logs.LogCollector;
@@ -23,17 +24,20 @@ public class JadxGUI {
 
 	public static void main(String[] args) {
 		try {
-			LogCollector.register();
-			JadxSettings settings = JadxSettingsAdapter.load();
-			settings.setLogLevel(LogHelper.LogLevelEnum.INFO);
-			// overwrite loaded settings by command line arguments
-			if (!settings.overrideProvided(args)) {
+			JadxSettings cliArgs = new JadxSettings();
+			JCommanderWrapper jcw = new JCommanderWrapper(cliArgs);
+			if (!jcw.parse(args) || !cliArgs.process(jcw)) {
 				return;
 			}
-			LogHelper.initLogLevel(settings);
+			LogHelper.initLogLevel(cliArgs);
 			LogHelper.setLogLevelsForDecompileStage();
+			LogCollector.register();
 			printSystemInfo();
 
+			JadxSettings settings = JadxSettingsAdapter.load();
+			// overwrite loaded settings by command line arguments
+			jcw.overrideProvided(settings);
+
 			LafManager.init(settings);
 			NLS.setLocale(settings.getLangLocale());
 			ExceptionDialog.registerUncaughtExceptionHandler();
diff --git a/jadx-gui/src/main/java/jadx/gui/settings/JadxSettings.java b/jadx-gui/src/main/java/jadx/gui/settings/JadxSettings.java
index 414bd0d4d..f16465f0a 100644
--- a/jadx-gui/src/main/java/jadx/gui/settings/JadxSettings.java
+++ b/jadx-gui/src/main/java/jadx/gui/settings/JadxSettings.java
@@ -154,6 +154,10 @@ public class JadxSettings extends JadxCLIArgs {
 		return jadxSettings;
 	}
 
+	public JadxSettings() {
+		this.logLevel = LogHelper.LogLevelEnum.INFO;
+	}
+
 	public void sync() {
 		JadxSettingsAdapter.store(this);
 	}
@@ -868,9 +872,4 @@ public class JadxSettings extends JadxCLIArgs {
 			useSourceNameAsClassNameAlias = UseSourceNameAsClassNameAlias.create(deobfuscationUseSourceNameAsAlias);
 		}
 	}
-
-	@Override
-	protected JadxCLIArgs newInstance() {
-		return new JadxSettings();
-	}
 }