Today I've committed some code that breaks compatibility in PDT 2.0: the
index file format has been changed.
This was a required step for improving performance in Code Assist. Here are
steps for returning to normal work:
1. Close all projects in your workspace.
2. Find index files under <your workspace
location>/.metadata/.plugins/org.eclipse.dltk.core/*.index
3. Delete index files.
4. Come back to Eclipse, and create an empty PHP project (this will
re-create index files for the PHP language model). Wait until it's built,
then you can remove it.
5. Open your projects.