OSGi guidelines allow for packing *.so in jars. Bundles with native code
can be installed as directories (I think it is a preferred way) or as
jars (and then are extracted at runtime into ~/.eclipse ).
I'd suggest checking what is the shape of the bundle (jar or dir) in ptp
installed from upstream (which will be processed by Eclipse P2
installation mechanism) and then either asking upstream to ship the
bundle as jar or unpacking the jar during building.
There is no support for installation preprocessing in Fedora Eclipse yet
(if you don't extract the bundle during build time it will not be
extracted at runtime).
In case of questions, ping me on irc.