jsPlumb's documentation is maintained in the associated wiki on GitHub, which is at git@github.com:sporritt/jsPlumb.wiki.git. A branch that matches the current dev branch is used; at release time this branch is merged into master and then you see it on GitHub.
Documentation is edited locally using Gollum (or by hand) as per the discussion on this page. During development, all of the Documentation links in the demo pages point to http://localhost:4567, as this is the default port on which Gollum runs.
The jsPlumb build script converts all the markdown files into html and inserts them into a final template, copying everything into dist/docs.
API documentation, from release 1.6.0, is being generated with YUIDoc, as part of the Grunt build.
The build places the API docs in dist/apidocs.