Here's an attempt to fix the issue by switching from two projects to one and update the new project to be more usable.
First, copy the 6.0 version of the project to a location without a version number:
svn cp tools/ide/netbeans/6.0/nbproject tools/ide/netbeans
Then remove the version-specific projects:
svn rm tools/ide/netbeans/5.5 tools/ide/netbeans/6.0
Finally, update the project using the attached patch (update-project.diff). The patch makes the following changes to the project definition:
1) Adjust the relative path to the project directory to account for the nbproject directory being moved up one level.
2) Modify classpath:
- Remove tools/java/xercesImpl.jar since it's no longer in the repository.
- Remove the classes directory since it's not needed and causes duplicate entries in the Go to type dialogue window.
3) Change source level from 1.4 to 1.5 to prevent error markers when working on code that uses generics or other 1.5 language features.
4) Add project-specific formatting so that you don't need to change the global formatting settings to get the correct tab size for Derby code.