diff --git a/setup/bootstrap.sh b/setup/bootstrap.sh
index 5326115..388ec6d 100755
--- a/setup/bootstrap.sh
+++ b/setup/bootstrap.sh
@@ -61,14 +61,24 @@ if ! command -v git &>/dev/null; then
     esac
 fi
 
-# Create shell directory if it doesn't exist
-mkdir -p "$HOME/shell"
-
 # Clone or update repository
-if [ -d "$DOTFILES_DIR" ]; then
+if [ -d "$DOTFILES_DIR/.git" ]; then
     echo -e "${YELLOW}Updating existing shell repository...${NC}"
     cd "$DOTFILES_DIR"
     git pull origin $DOTFILES_BRANCH
+elif [ -d "$DOTFILES_DIR" ]; then
+    echo -e "${YELLOW}Directory exists but is not a git repository.${NC}"
+    # Check if directory is empty
+    if [ -z "$(ls -A "$DOTFILES_DIR")" ]; then
+        echo -e "${YELLOW}Directory is empty. Cloning...${NC}"
+        git clone "https://github.com/$DOTFILES_REPO.git" "$DOTFILES_DIR"
+    else
+        echo -e "${YELLOW}Backing up existing directory...${NC}"
+        mv "$DOTFILES_DIR" "${DOTFILES_DIR}.bak.$(date +%s)"
+        echo -e "${YELLOW}Cloning shell repository...${NC}"
+        git clone "https://github.com/$DOTFILES_REPO.git" "$DOTFILES_DIR"
+    fi
+    cd "$DOTFILES_DIR"
 else
     echo -e "${YELLOW}Cloning shell repository...${NC}"
     git clone "https://github.com/$DOTFILES_REPO.git" "$DOTFILES_DIR"