Just some notes...
Make Sakai/uPortal run in the same Tomcat
Build two portlets: Sakai/iFrame and Sakai/JSR-168 - both effectively take a tool placement ID and render properly.
Sakai/JSR-168 makes "request.portlet.fragement" calls
Sakai/Iframe simply puts in the Charon URL into an iFrame
Make sakai "fragment source" which populates the structure under a tab based on the Sakai site/page/tool structure.
Make API-Only jars for uPortal and GAPs integration APIs
Make Sakai User Directory Provider which reads from uPortal's Person Attribute DAO in uPortal (person.jar)
Make Sakai tools appear as portlets in a portlet.xml so they can be published and scribed in the normal manner. Alter the iframe/jsr-168 portlets to self-instance and look to portlet roles such as admin/peon.
Make a GAPS plugin which causes any and all Sakai groups appear as uPortal Groups (place in in a tree structure in GAPs).
Make Sakai existing placements for tools appear as channels in a tree structure in GAPS (site/page/tool).
Switch to maven
Switch to SVN