Core team member Christophe Porteneuve has been hard at work for the past few months tracking and documenting Prototype for his new book Prototype and script.aculo.us, which is now available as a Beta Book from the Pragmatic Programmers (and is scheduled to ship later this year).
The second half, to be made available in the next beta release, will feature complete coverage of script.aculo.us.
If you buy the PDF (or PDF+Paper combo) now, you'll get access to updated versions of the book as they're made available, plus a copy of the final version once it's released.
Prototype and script.aculo.us is destined to become the bible of Prototype developers, so have a look at the sample chapters and purchase your beta copy today! :)