Troubleshooting

Ultimate does not compile (perhaps after you updated your working copy or just after your initial setup)

Refresh packages
In Eclipse's package explorer:
Mark all packages, then hit F5 (Refresh)
Note that if closed packages are marked, refresh will not work (but won't tell you that it did nothing). Either filter them out or mark only open packages.
Cleanup the build
Project->Clean..->Clean all projects->OK
Project->Build All (or Build automatically)
Check plugin dependencies
"Run" pulldown menu->Run configurations...
Choose your Run configuration
Go to Plugins tab
Click Validate plugins ()
If any problems are detected, check the boxes in the list for the plugins that are reported as unfulfilled dependencies
In Eclipse Mars, you have to uncheck "Include optional dependencies.." before clicking "Add required plugins". One should also remove the package org.eclipse.ui.trace, as this is not needed and just gives you trouble.
Import new projects
File->Import..
Existing Projects into workspace
select Ultimate's trunk/source folder
check all new plugins in the list (the ones not greyed out)
"Finish"
If there are errors in !ToolchainData.java during the build, the reason might be that xjc is not found. xjc is part of the Java SDK. Add /path/to/jdk/bin to your PATH environment variable and restart Eclipse.

Provide feedback