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[news.eclipse.tools.pdt] Code completion and ctrl-click: looking in wrong directory

I've recently moved a lot of code from one folder to another, and deleted the first folder. Now the code completion and Ctrl-Click is broken, because it will keep looking in the old folder.

Code completion only shows methods that were in the old version. Changes don't appear

Ctrl-click on methods doesn't do anything

Ctrl-click on classes shows me an option dialog, which shows the old and new class file.

I already hit refresh, and deleted the contents in .cache.

I'm using PDT 1.0.3 on Eclipse 3.3.2 and accessing my code on an FTP server through the RSE plugin.

Can I solve this, or is it a bug?