Edición: encontré la solución: edite el archivo core.jar, elimine todo el paquete excepto el paquete del códec y añádalo a la ruta de compilación, el paquete del códec debe estar en el contenedor, no puede ser el código fuente. código simple para Lucene, se ejecuta con Lucene core lib, pero causa un error cuando uso la fuente Core de Lucene.

public static void main(String[] args) throws IOException, ParseException {
    Analyzer analyzer = new StandardAnalyzer(Version.LUCENE_CURRENT);

    // Store the index in memory:
    Directory directory = new RAMDirectory();
    // To store an index on disk, use this instead:
    // Directory directory = FSDirectory.open("/tmp/testindex");
    IndexWriterConfig config = new IndexWriterConfig(
            Version.LUCENE_CURRENT, analyzer);
    IndexWriter iwriter = new IndexWriter(directory, config);
    Document doc = new Document();
    String text = "This is the text to be indexed.";
    doc.add(new Field("fieldname", text, TextField.TYPE_STORED));
    iwriter.addDocument(doc);
    iwriter.close();

    // Now search the index:
    DirectoryReader ireader = DirectoryReader.open(directory);
    IndexSearcher isearcher = new IndexSearcher(ireader);
    // Parse a simple query that searches for "text":
    QueryParser parser = new QueryParser(Version.LUCENE_CURRENT,
            "fieldname", analyzer);
    Query query = parser.parse("text");
    ScoreDoc[] hits = isearcher.search(query, null, 1000).scoreDocs;
    // Iterate through the results:
    for (int i = 0; i < hits.length; i++) {
        Document hitDoc = isearcher.doc(hits[i].doc);
                System.out.println(hitDoc.get("fieldname"));
    }
    ireader.close();
    directory.close();
}

El error es:

 Exception in thread "main" java.lang.ExceptionInInitializerError
        at org.apache.lucene.index.LiveIndexWriterConfig.<init>(LiveIndexWriterConfig.java:118)
        at org.apache.lucene.index.IndexWriterConfig.<init>(IndexWriterConfig.java:145)
        at Test.main(Test.java:34)
    Caused by: java.lang.IllegalArgumentException: A SPI class of type org.apache.lucene.codecs.Codec with name 'Lucene40' does not exist. You need to add the corresponding JAR file supporting this SPI to your classpath.The current classpath supports the following names: []
        at org.apache.lucene.util.NamedSPILoader.lookup(NamedSPILoader.java:104)
        at org.apache.lucene.codecs.Codec.forName(Codec.java:95)
        at org.apache.lucene.codecs.Codec.<clinit>(Codec.java:122)
        ... 3 more