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While working on bug 362227 it turned out that Resource#contains and Resource#isConflicting do not check if the other resource is stored in the same workspace. This not a problem at the moment, but in case we add multi-workspace support, two resources with the same path stored within different workspaces would be in conflict with each other.
Created attachment 206263 [details] Patch
Makes sense. Could you also write a test for it?
I assumed that the multi workspace work was merged into master. Check that the test pass and feel free to release the fix.
Thanks! Fixed in master.