Prototype is downloaded as one big file: prototype.js. "prototype.js is a composite file generated from many source files in the src/ directory."
Looks like we are using these source files, but there seems to be no source bundle available containing the source files.
Need to figure out how to check out the source files from their github first, but by just browsing the gitbub on the web, seems the source has quite different directory structure already. Our version is just a bunch of .js files in one directory.
Prototype 1.6.1 RC2 for IE8 compatibility. No RC release for Scriptaculous. 1.xx is feature-frozen. 1.8.3 will be a bugfix release that doesn't concern IE8. Scriptaculous 2 is "in the works". Not much info. on it.