Various clean-ups in preparation for release.

Fix theora_clear() so it actually clears an encoder instance.
Remove link-time dependencies of the decoder code on the encoder code.
This allows the separation of the two libraries, but requires a virtual
 function table of entry points into the encoder in order to work with the old
 libtheora API functions that don't distinguish between encoder and decoder
 objects.
Future upgrades will need to be careful of this bit to retain ABI
 compatibility.
Fix up #include directives to point directly to the project-local files they
 are including.
General warning clean-up.
Minor updates to the version script; this still needs to be fixed to use the
 proper version macros from configure.ac.

svn path=/trunk/theora/; revision=13596