I am using Eclipse 3.3 (\"Europa\"). Periodically, Eclipse takes an inordinately long time (perhaps forever) to start up. The only thing I can see in the Eclipse log is:
In my case (Juno) I had to do this:
find $WORKSPACE_DIR/.metadata/.plugins/org.eclipse.core.resources/.projects \
-name .indexes -exec rm -fr {} \;
That did the trick.
Initially I thought it was a problem with Mylyn (I experienced these freezes after I started using its generic web connector), but the problem appeared even after uninstalling the connector, and even deleting the .mylyn directories.
Edit: I also managed to restart eclipse by deleting just one file:
rm $WORKSPACE_DIR/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi
That worked fine, without any indexes involved. Only the workbech, which I personally don't mind that much.