diff --git a/clean_and_recreate_all b/clean_and_recreate_all
index 1b740f8..b9df6bc 100755
--- a/clean_and_recreate_all
+++ b/clean_and_recreate_all
@@ -1,6 +1,8 @@
 #!/bin/bash
 
 NO_PROMPT="false"
+CLEAN_ALL="false"
+RESTORE_MODIFIED="false"
 START_VITIS="false"
 IMPORT_HW_PLATFORM_ONLY="false"
 
@@ -9,6 +11,10 @@ REPO_INITIALIZED_FILE_EXISTS="false"
 for arg in "$@"; do
     if [ $arg == "--no-prompt" ]; then
         NO_PROMPT="true"
+    elif [ $arg == "--clean-all" ]; then
+        CLEAN_ALL="true"
+    elif [ $arg == "--restore-modified" ]; then
+        RESTORE_MODIFIED="true"
     elif [ $arg == "--start-vitis" ]; then
         START_VITIS="true"
     elif [ $arg == "--import-hw-platform-only" ]; then
@@ -16,23 +22,32 @@ for arg in "$@"; do
     fi
 done
 
+if ! [ -f ".repo_initialized" ]; then
+    echo "!!! INFO !!! It seems that you have not executed the 'init_after_clone' script. Please run it first!"
+    exit 1
+fi
+
 if [ $NO_PROMPT == "false" ]; then
     read -p "!!! WARNING !!! All unstaged and untracked files will be deleted! Press ENTER to continue or CTRL+C to abort..."
 fi
 
 echo "############################################################"
-echo "# Delete all unstaged and untracked files ..."
+echo "# Delete all untracked files ..."
 echo "############################################################"
-if [ -f ".repo_initialized" ]; then
-    REPO_INITIALIZED_FILE_EXISTS="true"
-    rm -f .repo_initialized
+
+if [ $CLEAN_ALL == "true" ]; then
+    git clean -dfx -e "/.repo_initialized"
+else
+    git clean -dfx -e "/.repo_initialized" -e "/.metadata/.plugins/org.eclipse.core.runtime" -e "/.metadata/.plugins/org.eclipse.debug.core" -e "/.metadata/.plugins/org.eclipse.tcf.debug"
 fi
 
-git clean -dfx
+if [ $RESTORE_MODIFIED == "true" ]; then
+    echo "############################################################"
+    echo "# Restore all unstaged files ..."
+    echo "############################################################"
 
-if [ $REPO_INITIALIZED_FILE_EXISTS == "true" ]; then
-    touch .repo_initialized
-    echo "This file is checked by the 'init_after_clone' script." >> .repo_initialized
+    git restore .
+    git submodule update --recursive
 fi
 
 echo "############################################################"
@@ -59,9 +74,11 @@ fi
 
 # Disable Vitis welcome screen
 FILE=".metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.prefs"
-touch $FILE
-echo "eclipse.preferences.version=1" >> $FILE
-echo "showIntro=false" >> $FILE
+if ! [ -f $FILE ]; then
+    touch $FILE
+    echo "eclipse.preferences.version=1" >> $FILE
+    echo "showIntro=false" >> $FILE
+fi
 
 echo "############################################################"
 echo "# ... finished!"