Classe File e criar pastas

// Cria channel na origem
FileChannel oriChannel = new FileInputStream(?Caminho Origem?).getChannel();
// Cria channel no destino
FileChannel destChannel = new FileOutputStream(?Caminho Destino?).getChannel();
// Copia conteúdo da origem no destino
destChannel.transferFrom(oriChannel, 0, oriChannel.size());

// Fecha channels
oriChannel.close();
destChannel.close();

//Caminho do arquivo original
		File pathAtual = new File("/home/linux/a.txt");
		
		//Caminho a ser criado: /home/linux/file/home/linux/
		File pathNovo = new File("/home/linux/file/"+pathAtual.getParent());
		
		//Arquivo no novo diretorio : /home/linux/file/home/linux/a.txt
		File newArk = new File(pathNovo+"/"+pathAtual.getName());
		if(!pathNovo.isDirectory()){
			pathNovo.mkdirs();
			newArk.createNewFile();
		}else{
			newArk.createNewFile();
		}
		
		FileInputStream inputStream = new FileInputStream(pathAtual);
		FileOutputStream outputStream = new FileOutputStream(newArk);
		
		byte[] bs = new byte[(int) pathAtual.length()];
		int line = 0;
		while((line=inputStream.read(bs)) != -1){
			outputStream.write(bs, 0, line);
		}
		
		inputStream.close(); outputStream.close();