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Thanks for the project. I tried again to reproduce, but everything is still working fine for me.
There is another possibility. Are you using a custom GRAILS_ROOT path variable? When you go to Project -> Properties -> Resources -> Linked Resources -> Path Variables, you should see something like "/Users/andrew/.grails" (or something similar on windows).
If the GRAILS_ROOT points to somewhere non-existant or just incorrect, this may cause problems. Although that being said, I tried to cause a similar problem by forcing a bad GRAILS_ROOT, but the import process fixed itself. So, I'm still not really sure.
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I'm going to try Groovy/Grails tool suite. I didn't even notice it's available. For now I've been using Spring tool suite.