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libav tries to ship a compatible wrapper called ffmpeg and a redone one called avconv. But ffmpeg itself just ships ffmpeg and puts incompatible changes in there, so you'd actually be worse off.

What issues were you having, and with what file types?

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Incompatible? Do you mean with libav?

Backwards incompatible with previous versions of itself.

Most of the old options have been mapped to the new interface (see opt_old2new() for instance). So most of the old commands are still compatible. Libav also has dropped ffmpeg forked copy since a long while, so FFmpeg is actually more retro compatible.

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