Remove include.xml and improve .xml-template

- Includes a temp fix for #469 by disabling the flixel preloader by default for now.
- Removes the `include.xml` and moves its contents into the template xml.
- Renamed the `thread` flag to `FLX_THREADING` to follow the naming conventions
- Removed the `<setenv name="no_console" value="1" />` flag since it doesn't seem to do anything.
- Reorganized a few things and improved documentation.