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For Sakai 2.0, the compatible Tomcat version has now been determined to be 5.5.x, thus this needs to be accounted for in the design process.
AUTHENTICATION PROCESS (Sakai 1.5.0,1.5.1)
In summary, Sakai allows for Tomcat container authentication ("container.auth" setting in sakai.properties) to be enabled as well as customization of various interfaces (UserDirectoryProvider in particular) within Sakai to support authentication. Sakai authentication is now supporting an LDAPDirectoryProvider, and with each provider interface there are options to edit/store/ and modify users. By setting the "container.auth" parameter accordingly, Sakai is configured to trust remote user.
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