I recently upgraded to the latest version of Eclipse + PDT. For some reason, the “jump to function definition” command was not woking anymore. Once you’re used to it, there’s no going back. Command-clicking on a function to automatically open its file and definition is so time saving I could not imaging working without it any more.

Hopefully I finally found this article by Adrian Schneider that explained how to solve this issue.

Simply shut down Eclipse, delete the .metadata/.plugins/org.eclipse.dltk.core.index.sql.h2 folder in your workspace and restart Eclipse. This will force the DLTK indexer to rebuild its database. That solved the issue for me!