matroskaenc: cosmetics, reorder the #includes
matroskaenc: add an option to put the index at the start of the file
avconv: improve -re implementation

Integrate the code in the packet reading function, instead of inserting
sleeps in many places.
This is simpler to follow and should work better.
avconv: do not send non-monotonous DTS to the muxers.

Hack partially based on a commit by Michael Niedermayer <michaelni@gmx.at>
Should fix (or work around) bug 458.