I'm not quite sure if you understand you, but here it goes.
Well, running / debugging OSGi applications in Eclipse is very easy if your packages are in projects with PDE support, or at least are on your target platform.
Do you have a source for all of your packages? Sourceless debugging is not that useful. If you do, can you just import the entire source of your packages into the Eclipse workspace?
Otherwise, you can create a target platform, add all your packages to it. (as the first attempt, I would say, dump all your packages in the directory and specify the target platform there)
In any case, you should be able to run (or debug) โ OSGi framework โ Create โ Select your packages โ Start
You can choose packages or a target platform from your workspace.
source