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If you "Organize Imports" on a bunch of read-only files and the project isn't shared the resulting dialog tells you of all the files that were read-only. There should be an option to make the files writable and continue with the operation.
If we follow that pass we should do it for all actions (Organize imports, refactorings, format). Best would be to have a special "team provider" for this and hook it into validateEdit. To be considered for 3.1
This is not only a JDT/UI issue. All actions that operate on file content (Platform/UI, CDT, JDT, WTP,...) should behave the same way then. A special team provider would do this for all code manipulation operations that do a validateEdit (which should be all of them). Moving to Platform/Core for comments since such a provider is best provided by Core Resources.
This has been fixed in Eclipse 3.1 stream. *** This bug has been marked as a duplicate of 28218 ***