Reland "Fixes to the the activity flag that is passed to Silk so it represents...

Reland "Fixes to the the activity flag that is passed to Silk so it represents the final activity flag used in the DTX decision"

This flag was modified after calling the Silk encoder function. This commit corrects that behavior by introducing those modifications before calling the Silk encoder.

Slightly modified comments by Felicia Lim

Signed-off-by: Felicia Lim <flim@google.com>