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When there are multiple projects with dependencies with each other, Rebuild all doesn't follow the dependencies and builds sometime a dependant project after the project on which it depends
Do you mean when you have cycles in the project classpaths ? If so, this is a known issue. Which build are you using ? In 2.1M3, this behavior should have been improved already.
Ludovic - any update ? Did you have cycles ? Unless we get more information, we cannot do anything.
Assuming cycles are involved, this defect should get fixed once basic support for cycle is added to Java builder.
*** This bug has been marked as a duplicate of 20614 ***