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There was existing code base, and I wanted to use NetBeans 4.0 test whether I could integrate it with the existing code. After creating a new project for netbeans (with project directory and source directory in completely different folders but within the same drive), I assigned library and compiler which are yet in completely different directories but the same drive. Then, I clicked "apply" button to get the error dialog box.
Created attachment 18172 [details] error log created after the exception.
*** This issue has been marked as a duplicate of 50134 ***
THis issue is not a duplicate of issue 50314
You are right. This problem seems to be caused by a bug in MDR caches we had in beta 2. This bug resulted in a severe metadata repository corruption. To recover, one needs to shutdown netbeans and delete var/cache/mdrstorage directory from NB user directory. This bug was fixed several weeks ago, so this should no longer happen in daily builds.