Add an ini writer that respects the file structure and the comments that may be
already present in the config file. Move Application/Config.php into
Config/Config.php.
refs #4352
The constructor of the class is now private, instantiation happens
with Url::fromRequest and Url::fromPath. Also updated all occurences
of Url and fixed the Qlink helper to not overwrite the baseUrl with null
values
refs #4381