Also, tried to clean up the code formatting according to the guidelines
_and_ added (most) entries for PHPDoc.

Added a third parameter to $app->log() function in server part to turn off logging to database and use this option in mysql lib to not log any server side SQL errors to the database.

and make changes to mysql users in the mysql plugin module.

Refs: 1722

Also removed the calls to the db closeConn calls in favor of
destryong the connections on the class __destruct() 's..

Since firebird db had a closeConn as well, changed its __destruct
to calls its own personal closeConn which otherwise left unmodified.

Refs: 1722

1) Added DEVSYSTEM define in config.inc.php.master  defaults to 0
  If set to 1 classes can load as symbolc links, server.php now

2) server.php now resolves its require()ed files with an absolute
   path instead of relative.

- replace double-quotes with single-quotes whenever appropriate

Added a missing language string in server config form.

- fixed a php notice in app.inc.php

- Changed the default settings for websites

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