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A recent change in CDT 7.0 causes a refresh local for a resource that doesn't exist in the workspace (because it is filtered out), but exist in the file system nonetheless. The proper fix will be in the core.resources to prevent clients from doing so, but in the mean time, the CDT can be patched to avoid this bug as well (see included patch).
Created attachment 172888 [details] JUnit test
Created attachment 172889 [details] Fix
*** Bug 321205 has been marked as a duplicate of this bug. ***
Now fixed on the R3_6_maintenance branch, in the following plugins: org.eclipse.core.resources org.eclipse.core.tests.resources
Verified in M20100901-1310