Intermediate commit while still debugging.

Currently updating recent features to make them work with file merging.

Also, replaced the YUI-based data visualizations with ones based on D3JS.
Debugged code for merging logs, correcting the bugs introduced by all the improvements required to get the module widget working, as well as new bugs uncovered by the more aggressive demands on example 7. Merging of modules does not yet work.
Modules and merging are fully working.