diff --git a/src/main/java/org/jsweet/JSweetCommandLineLauncher.java b/src/main/java/org/jsweet/JSweetCommandLineLauncher.java
index 37c3f17d..c1b06428 100644
--- a/src/main/java/org/jsweet/JSweetCommandLineLauncher.java
+++ b/src/main/java/org/jsweet/JSweetCommandLineLauncher.java
@@ -81,8 +81,9 @@ public class JSweetCommandLineLauncher {
 			Util.addFiles(".java", inputDir, files);
 
 			JSweetTranspiler transpiler = new JSweetTranspiler(tsOutputDir, jsOutputDir, classPath);
-			transpiler.setBundle(jsapArgs.getBoolean("bundle"));
 
+			transpiler.setBundle(jsapArgs.getBoolean("bundle"));
+			transpiler.setNoRootDirectories(jsapArgs.getBoolean("noRootDirectories"));
 			File bundlesDirectory = null;
 			if (jsapArgs.getFile("bundlesDirectory") != null) {
 				bundlesDirectory = jsapArgs.getFile("bundlesDirectory");
@@ -90,25 +91,13 @@ public class JSweetCommandLineLauncher {
 			}
 			logger.info("bundles directory: " + bundlesDirectory);
 			transpiler.setBundlesDirectory(bundlesDirectory);
-
 			transpiler.setPreserveSourceLineNumbers(jsapArgs.getBoolean("debug"));
-			if (args.length > 4) {
-				File f = new File(args[4]);
-				if (f.exists()) {
-					transpiler.setTsDefDirs(f);
-					logger.info("tsdef dir: " + args[4]);
-				} else {
-					OUTPUT_LOGGER.warn("tsdef dir does not exist - " + args[4]);
-				}
-			}
-
 			transpiler.setModuleKind(ModuleKind.valueOf(jsapArgs.getString("module")));
+			transpiler.setEncoding(jsapArgs.getString("encoding"));
 
 			ErrorCountTranspilationHandler transpilationHandler = new ErrorCountTranspilationHandler(new ConsoleTranspilationHandler());
 			errorCount = transpilationHandler.getErrorCount();
 
-			transpiler.setEncoding(jsapArgs.getString("encoding"));
-
 			transpiler.transpile(transpilationHandler, SourceFile.toSourceFiles(files));
 
 			errorCount = transpilationHandler.getErrorCount();
@@ -159,6 +148,14 @@ public class JSweetCommandLineLauncher {
 		optionArg.setHelp("An input dir containing Java files to be transpiled.");
 		jsap.registerParameter(optionArg);
 
+		// Skip empty root dirs
+		switchArg = new Switch("noRootDirectories");
+		switchArg.setLongFlag("noRootDirectories");
+		switchArg.setHelp(
+				"Skip the root directories (i.e. packages annotated with @jsweet.lang.Root) so that the generated file hierarchy starts at the root directories rather than including the entire directory structure.");
+		switchArg.setDefault("false");
+		jsap.registerParameter(switchArg);
+
 		// TypeScript output directory
 		optionArg = new FlaggedOption("tsout");
 		optionArg.setLongFlag("tsout");
diff --git a/src/main/java/org/jsweet/transpiler/JSweetTranspiler.java b/src/main/java/org/jsweet/transpiler/JSweetTranspiler.java
index bb3a98c4..c56cfa64 100644
--- a/src/main/java/org/jsweet/transpiler/JSweetTranspiler.java
+++ b/src/main/java/org/jsweet/transpiler/JSweetTranspiler.java
@@ -132,6 +132,7 @@ public class JSweetTranspiler {
 	private boolean bundle = false;
 	private File bundlesDirectory;
 	private String encoding = null;
+	private boolean noRootDirectories = false;
 
 	/**
 	 * Creates a JSweet transpiler, with the default values.
@@ -773,7 +774,8 @@ public class JSweetTranspiler {
 				String cuName = s[s.length - 1];
 				s = cuName.split("\\.");
 				cuName = s[0];
-				String outputFileRelativePathNoExt = cu.packge.fullname.toString().replace(".", File.separator) + File.separator + cuName;
+				String packageName = isNoRootDirectories() ? Util.getRootRelativeJavaName(cu.packge) : cu.packge.getQualifiedName().toString();
+				String outputFileRelativePathNoExt = packageName.replace(".", File.separator) + File.separator + cuName;
 				String outputFileRelativePath = outputFileRelativePathNoExt + printer.getTargetFilesExtension();
 				logger.info("output file: " + outputFileRelativePath);
 				File outputFile = new File(tsOutputDir, outputFileRelativePath);
@@ -1236,4 +1238,24 @@ public class JSweetTranspiler {
 	public void setEncoding(String encoding) {
 		this.encoding = encoding;
 	}
+
+	/**
+	 * Tells if this transpiler skips the root directories (packages annotated
+	 * with @jsweet.lang.Root) so that the generated file hierarchy starts at
+	 * the root directories rather than including the entire directory
+	 * structure.
+	 */
+	public boolean isNoRootDirectories() {
+		return noRootDirectories;
+	}
+
+	/**
+	 * Sets this transpiler to skip the root directories (packages annotated
+	 * with @jsweet.lang.Root) so that the generated file hierarchy starts at
+	 * the root directories rather than including the entire directory
+	 * structure.
+	 */
+	public void setNoRootDirectories(boolean noRootDirectories) {
+		this.noRootDirectories = noRootDirectories;
+	}
 }