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If a processor tries to create a file that already exists in the workspace, a compiler NPE occurs. This should instead result in a FilerException being thrown to the processor.
I think overwriting "files that exist in the workspace" (or at least derived files) should be okay, because they might have been generated by APT in previous builds. What's forbidden is overwriting files that were produced during the current build. Both these scenarios need to be checked; the first should be supported, the second should produce a FilerException.
Bug 320195 addresses the second issue (attempting to overwrite a generated file in the same compile).
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.