In order to get from a set of package imports and exports to a list of bundles which can be used for compilation, you'll need some sort of repository of candidate bundles, and a provisioner to work out which bundles best provide which packages. If you're using 'Require-Bundle' (not a best practice), you'll know the bundle names, but not necessarily the versions, so some provisioning is still required.
For example, in Eclipse PDE, the target platform is used as the basic repository for compilation. You can also do more sophisticated things like using Eclipse's p2 provisioning to provision your target platform, so you can use an external p2 repository as your repository instead of setting one up yourself. For command line builds, Tycho allows Maven builds to use the same sort of mechanisms for resolving the classpath as Eclipse itself uses.
An alternative approach is to list your 'classpath' as Maven dependencies, and let the maven bundle plugin (based on bnd) generate your manifest for you.
If you can't take advantage of existing command line tools because you're compiling programatically (it's not entirely clear from your question what problem you're trying to solve), your best best is probably to take advantage of an existing provisioning technology, like OBR, Eclipse p2, or Apache Ace to work out the bundles which should be on the class path for compilation.