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M20060712-0922 (3.2) Organize Manifests adds .settings and META-INF to Export-Package. To reproduce, apply action to org.junit4 R3_2.
ok, fixed. The problem was coming from the first checkbox in the organize manifest wizard. This button adds all packages in your project to the export-package header. Since the jar in the project is on the buildpath, the folders in it (.settings and META-INF) were added. The fix is to filter out META-INF as a special case while also not adding any folders who start with '.'. Modified org.eclipse.pde.internal.ui.wizards.tools.OrganizeManifest v 1.7. Should be in 3.3 M1
D'oh, this is a bit complicated... . There was a bug in jdt.core which made folders with invalid package names in jars appear as IPackageFragments. This has been fixed in HEAD (but the fix still a bit controversial). With I20060718-0800, the tricks in PDE are not required any more, since those folders are no longer considered as packages. Final solution depends on outcome of bug 148944. I'd suggest to revert the fix again for now. Sorry for the hassle, but I wasn't aware of that jdt.core problem.
Brian, I agree with Markus. The fix in PDE did not look right to me.
I guess I was on a roll fixing bugs and fixed something I shouldn't have :)
will close since we reverted the change.