EDIT

<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="-webapp=${workspace_loc:cdmlib-remote-webapp/src/main/webapp/}&#10;-webappClasspath=${project_classpath:cdmlib-remote-webapp}&#13;&#10;-jmx"/>

import static eu.etaxonomy.cdm.server.CommandOptions.WEBAPP_CLASSPATH;

    private String webAppClassPath = null;

        // WEBAPP options

        //   prepare web application files to run either from war files (production mode)

        //   or from source (development mode)

        if(cmdLine.hasOption(WEBAPP.getOpt())){

            cdmRemoteWebAppFile = new File(cmdLine.getOptionValue(WEBAPP.getOpt()));

            if(cdmRemoteWebAppFile.isDirectory()){

                logger.info("using user defined web application folder: " + cdmRemoteWebAppFile.getAbsolutePath());

            } else {

                logger.info("using user defined warfile: " + cdmRemoteWebAppFile.getAbsolutePath());

            // load the default-web-application from source if running in development mode mode

            if(isRunningFromCdmRemoteWebAppSource()){

                //TODO check if all local paths are valid !!!!

               defaultWebAppFile = new File("./src/main/webapp");

            } else {

               defaultWebAppFile = extractWar(DEFAULT_WEBAPP_WAR_NAME);

            }

            if(isRunningFromCdmRemoteWebAppSource()){

                if(cmdLine.hasOption(WEBAPP_CLASSPATH.getOpt())){

                    String classPathOption = cmdLine.getOptionValue(WEBAPP_CLASSPATH.getOpt());

                    normalizeClasspath(classPathOption);

//                    webAppClassPath = classPathOption;

                }

            }

        } else {

            // read version number

            String version = readCdmRemoteVersion();

            cdmRemoteWebAppFile = extractWar(CDMLIB_REMOTE_WEBAPP + "-" + version);

            defaultWebAppFile = extractWar(DEFAULT_WEBAPP_WAR_NAME);

        }

        // HTTP Port

        int httpPort = 8080;

        if(cmdLine.hasOption(HTTP_PORT.getOpt())){

            try {

               httpPort = Integer.parseInt(cmdLine.getOptionValue(HTTP_PORT.getOpt()));

               logger.info(HTTP_PORT.getOpt()+" set to "+cmdLine.getOptionValue(HTTP_PORT.getOpt()));

           } catch (NumberFormatException e) {

               logger.error("Supplied portnumber is not an integer");

               System.exit(-1);

           }

        }

    /**

     * @param classpath

     */

    private void normalizeClasspath(String classpath) {

        StringBuilder classPathBuilder = new StringBuilder((int) (classpath.length() * 1.2));

        String[] cpEntries = classpath.split("[\\:]");

        for(String cpEntry : cpEntries){

            classPathBuilder.append(',');

//            if(cpEntry.endsWith(".jar")){

//                classPathBuilder.append("jar:");

//            }

            classPathBuilder.append(cpEntry);

        }

        webAppClassPath = classPathBuilder.toString();

    }

//            String classPath = System.getProperty("java.class.path");

//            logger.info("Running cdmlib-remote-webapp from source folder:, thus adding system property 'java.class.path=" + classPath +"'  to WebAppClassLoader");

//            classLoader.addClassPath(classPath);

            if(webAppClassPath != null){

                logger.info("Running cdmlib-remote-webapp from source folder: Adding class path supplied by option '-" +  WEBAPP_CLASSPATH.getOpt() +" =" + webAppClassPath +"'  to WebAppClassLoader");

                classLoader.addClassPath(webAppClassPath);

            } else {

                throw new RuntimeException("Classpath cdmlib-remote-webapp for missing while running cdmlib-remote-webapp from source folder. Please supplied cdm-server option '-" +  WEBAPP_CLASSPATH.getOpt() +"");

            }

                    "If this option is used extracting the war from the cdmserver jar file is omitted.\n \n" +

                    "DEVELOPMENT MODE:\n" +

                    "  If the specified path points to a directory the cdm-server will run in development mode.\n" +

                    "  In development mode the default webapplication containing the cdm-server management web \n" +

                    "  interface will be loaded from the source folder cdm-server/src/main/webapp. In normal \n" +

                    "  mode the default-webapp.war file will be used insead.\n" +

                    "  Using the following paths developers can run the cdmlib-remote-webapp instaces completely\n" +

                    "  from the target folder or from source (examples are for the eclipse ide):\n" +

                    "   - run from maven target: '{cdmlib-project-root}/cdmlib-remote-webapp/target/cdmserver'\n " +

                    "   - run from source: '{cdmlib-project-root}/cdmlib-remote-webapp/src/main/webapp'\n" +

                    "     When running from source you must also set the webapp-classpath option: \n" +

                    "     -webappClasspath=${project_classpath} " )

  @SuppressWarnings("static-access")

    public static final Option WEBAPP_CLASSPATH = OptionBuilder

            .withArgName("classpath")

            .hasArg()

            .withDescription("Sets the classpath for the cdmlib-remote-webapp instance when running from source code." +

                    " See option -webapp")

            .create("webappClasspath");

        .withArgName("datasourcesfile")

        .hasArg()

        .withDescription( "use the specified datasources file. Default is {user.home}/.cdmLibrary/datasources.xml")

        .create("datasources");

            options.addOption(WEBAPP_CLASSPATH);