encoder: merge common encoding code

Refactors out the common code from video and audio encoding/flushing
into a single method. This reuses code instead of duplicating it.

The method is public in the hopes of being able to reuse MediaEncoder
elsewhere in the codebase.

Allow caller to specify the stream index for the future case that the
AVFormatContext contains multiple streams (recording video and audio).

Change-Id: Ieae52bc453ef66d141a40819ca10fedbd38d9a86
Reviewed-by: Sebastien Blin <sebastien.blin@savoirfairelinux.com>