public  void index(File root,
    boolean create,
    String index) 
{
        try
        {
            Date start = new Date();
            writer = new IndexWriter(index, new StandardAnalyzer(), create, IndexWriter.MaxFieldLength.LIMITED);
            if (!create)
            {                 // delete stale docs
                deleting = true;
                indexDocs(root, index, create);
            }
            indexDocs(root, index, create);       // add new docs
            System.out.println("Optimizing index...");
            writer.optimize();
            writer.close();
            Date end = new Date();
            System.out.print(end.getTime() - start.getTime());
            System.out.println(" total milliseconds");
        }
        catch( Exception e )
        {
            e.printStackTrace();
        }
}

This will index a directory.

 public static  void main(String[] argv) 
{
        String index = "index";
        boolean create = false;
        File root = null;
        String usage = "org.apache.pdfbox.searchengine.lucene.IndexFiles [-create] [-index < index >] < root_directory >";
        if (argv.length == 0)
        {
            System.err.println("Usage: " + usage);
            return;
        }
        for (int i = 0; i <  argv.length; i++)
        {
            if (argv[i].equals("-index"))
            {         // parse -index option
                index = argv[++i];
            }
            else if (argv[i].equals("-create"))
            {     // parse -create option
                create = true;
            }
            else if (i != argv.length-1)
            {
                System.err.println("Usage: " + usage);
                return;
            }
            else
            {
                System.out.println( "root=" +argv[i] );
                root = new File(argv[i]);
            }
        }
        IndexFiles indexer = new IndexFiles();
        indexer.index( root, create, index );
}

This is the main entry point for the indexer.