I have just upgraded to Eclipse Juno 4.2. I have a completely clean new workspace, but have imported projects that have previously been used in Eclipse 3.7 and therefore have so
set eclipse_dir=D:\eclipse\release
mkdir %eclipse_dir%\disabled
mkdir %eclipse_dir%\disabled\features
mkdir %eclipse_dir%\disabled\plugins
move %eclipse_dir%\plugins\org.eclipse.jpt.* disabled\plugins
for /f %%i in ('dir features\org.eclipse.jpt.*" /ad /b') do (
move features\%%i" "%eclipse_dir%\disabled\features\%%i"
)