How do I use the fade in, fade out commands?

Within the format tag, you can now specify the duration and length of the fade that you would like to apply to your encodes. 

via XML:

<format>
   <fade_in>[FadeInStart]:[FadeInDuration]</fade_in>
   <fade_out>[FadeOutStart]:[FadeOutDuration]</fade_out>
</format>

Definitions:

FadeInStart: Start of fade_in effect in seconds

FadeInDuration: Duration of fade_in effect in seconds

FadeOutStart: Start of fade_out effect in seconds. If you specify this parameter equal to 0, fade out effect will be applied to the end of video/audio.

FadeOutDuration: Duration of fade_out effect in seconds.

Note: FadeIn/FadeOut effect applies both for audio and video streams.