OPENDJ-1714 (CR-6442) Refactor ConfigureDS.java

* ConfigureDS.java
** Made ConfigureDS call non static to allow methods extraction
** Extracted methods:
*** initializedArguments()
*** parseArguments()
*** checkGlobalArguments()
*** checkPortArguments()
      Use a loop instead of code duplication in this method
*** updateBaseDNs(baseDNs);
*** updateLdapPort();
*** updateAdminConnectorPort();
*** updateLdapSecurePort();
*** updateJMXport();
*** updateStartTLS();
*** updateKeyManager();
*** updateTrustManager();
*** updateRootUser(rootDN, rootPW);
*** addFQDNDigestMD5();
*** updateCryptoCipher();
*** writeUpdatedConfiguration();
*** initializeDirectoryServer()
** In key and trust provider related check/update config methods:
*** Create common method for both when it was possible
*** Extracted more little method to prevent code redundancy
** Add a custom ConfigureDSException to handle error message print
** Inline some local variables
** Format the whole file