I have added to CVS first public version of the manual, plus latex  
sources.  It's at ec/docs/manual/manual.pdf

If you don't have CVS, you can download it (temporarily) at http://cs.gmu.edu/~sean/temp/manual.pdf

The manual reflects the ECJ implementation out on CVS: this has many  
differences from the current snapshot.  In a few days (crossing  
fingers) we'll have a new snapshot out on the website along with a  
more permanent location for the manual.

Note that exactly one package is undocumented in the manual: the  
Particle Swarm Optimization package.  I do not trust this package and  
will be heavily revising it in the near future.

Hope this is useful to people: the manual documents practically  
everything in the system including many things you may not be aware of.

Sean