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A long time ago it has been decided that support for fragments will be limited in PDE. Fragments classes/packages are not visible in the PDE unless the host plugin has certain manifest flag set. Note that this flag (Eclipse-ExtensibleAPI) is Eclipse specific, and therefore should not be used by OSGi plugins. It would be good to properly support fragments in all aspects - the OSGi fragments are pretty powerful mechanism, and advanced users should have a possibility of leveraging them not only for delivering platform specific resources but rather for hacking/exporting unexported packages/exposing classes for tests etc etc.
I opened this bug before, sorry. *** This bug has been marked as a duplicate of bug 340546 ***