Rid uploaded scripts of DOS newlines if they have them
(cherry picked from commit e598ffadf14d50c686d185817a2e0bcf28424537)

We should be able to convert this to use something like the following:

$file = file_get_contents("filename");
$file = str_replace("\r", "", $file);
file_put_contents("filename", $file);
Since a setting was added for the settingsFile, we must store it from the command line argument otherwise after forcing a custom config, we parse it and ignore it later in a function that tries creating the default filename.
(cherry picked from commit a92c1dfe81efd8f4411da841b36f17f08d439eb6)

Conflicts:
	src/settings.c