Updated doc pages.
Made fixes to console highlighting.
Updated documentation files.
Moved sphinxext folder and updated configuration files.
Updated reference documentation.
Moved nmd file functions into a separate module, and added format doc.
Updated doc files.
Updated reference manual.
Added sequence analysis tutorial.
Updated documentation.
Revised doc javascript files.
Added new css files.
Updated tutorial pages.
Revised docstrings.
Revised docstrings.
Revised logo updater.
PCA calculations output PDB file always to include atom name/etc. in NMD.
Made changes for jQuery 1.9/2.0 compatibility.
Updated documentation pages.
Resolved reference problems.