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After using M2E / Ycho interactively all *,target files are likely to acquite target/... duplicates. These duplicates bloat the Window->Preferemces->PDE->TargetPlatform dialog and no doubt all other facilities that consider potential target platforms. Unfortunately the M2E project declines to mark such duplicates as derived, Bug 384356. It is therefore the responsibility of all code that might encounter such duplicates to ignore them.
Target Platforms are provided by PDE, so lets move the issue over there.
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.
Still awaiting triage by a relevant committer.