No, I don't skip them because further are things which makes duplicates.
For now I just clear index just before starting session factory:
so I make in Spring:
Code:
   <bean name="removeIndex" class="com.test.RemoveIndex" init-method="init">
      <property name="indexBase"><value>${indexBase}</value></property>
      <property name="createDatabase"><value>${hibernate.hbm2ddl.auto}</value></property>
   </bean>
    <bean id="sessionFactory" class="org.springframework.orm.hibernate3.annotation.AnnotationSessionFactoryBean" depends-on="removeIndex">
</bean>
And delete directory in RemoveIndex class:
Code:
public class RemoveIndex {
   
   private static final String SVN = ".svn";
   private String indexBase;
   
   private static final String HIBERNATE_CREATE = "create";
   private String createDatabase;
   public void init() {
      if(createDatabase.equals(HIBERNATE_CREATE)){
         File[] files = new File(indexBase).listFiles();
         for(File file : files) {
            if(!file.getName().equals(SVN)) {
               deleteDirectory(file);
            }
         }
      }
   }
   
   public static boolean deleteDirectory(File path) {
       if( path.exists() ) {
         File[] files = path.listFiles();
         for(int i=0; i<files.length; i++) {
            if(files[i].isDirectory()) {
              deleteDirectory(files[i]);
            }
            else {
              files[i].delete();
            }
         }
       }
       return( path.delete() );
     }
   
   public String getIndexBase() {
      return indexBase;
   }
   public void setIndexBase(String indexBase) {
      this.indexBase = indexBase;
   }
   public String getCreateDatabase() {
      return createDatabase;
   }
   public void setCreateDatabase(String createDatabase) {
      this.createDatabase = createDatabase;
   }
}
Maybe someone can provide better solution but this works for me perfectly now, and maybe helps someone in future.
Best regards,
Adr