av1_apply_encoding_flags() was called in encoder_encode(). If
lag_in_frames > 0, it wouldn't be called for last several frames
while flushing the encoder, and thus cpi->ref_frame_flags can not
be set correctly. This patch fixed the issue by adding an extra
flag cpi->ext_ref_frame_flags to store the external reference
frame flag, and pass it to cpi->ref_frame_flags correctly.

Change-Id: I9c3f22f92b81c7b4b6241a3f7edcaeabd8d8bbc9