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If we are removing linked resources, we actually modify .project file. ltk should check if .project is read-only and if it is true, we should ask to make .project writable or cancel the operation. I guess that the right place is ReadOnlyResourceFinder#hasReadOnlyResourcesAndSubResources and #confirmOperationOnReadOnlyElements which ignore linked resources at the moment.
On the other hand, for non-experienced users it may be not obvious why to modify .project permissions to delete a linked resource...
This bug hasn't had any activity in quite some time. Maybe the problem got resolved, was a duplicate of something else, or became less pressing for some reason - or maybe it's still relevant but just hasn't been looked at yet. If you have further information on the current state of the bug, please add it. The information can be, for example, that the problem still occurs, that you still want the feature, that more information is needed, or that the bug is (for whatever reason) no longer relevant. -- The automated Eclipse Genie.