Determine custom vendor dir if vendor-dir is added/changed

Fixed #1347
I prefer to keep the number of global constants to a minimum. Can you move this to a value in the Dependency Injection container?

Since you will need this value to initialize the JmsSerializer Service provider I recommend adding a new optional parameter 'options' to the Application constructor and set those values on the container after the parent constructor has been invoked. (thus on line 63 of the Application class: https://github.com/phpDocumentor/phpDocumentor2/blob/develop/src/phpDocumentor/Application.php#L63).

Because the DOMPDF code cannot reach the container I recommend moving that code (https://github.com/phpDocumentor/phpDocumentor2/blob/develop/src/phpDocumentor/Application.php#L32) to the Bootstrap class before the autoloader creation. This code is required to be included by DOMPDF before the autoloader triggers (that's why it was there)