Significantly revamped the Coq partition scanner

Files can now end with incomplete partitions, and splitting partitions over
several lines now works much more reliably
Added a preference to control PIDE processing annotations

Since these annotations have awful performance on Mac OS X, this option is
off by default. This commit also tidies up the rest of the preference
management code
Bumped the version numbers to 0.4.6.4 and added a changelog entry