The CDK IO format definitions and matchers are quite useful outside the scope of just the CDK library, for example, for the core of Bioclipse. The IChemFormatMatcher implementations indeed do not depend on 'interfaces' or 'core' modules.
Only complication is that TestMethod and TestClass are being used, as well as DataFeatures. I have moved these into a second new module 'annotation' as they deal with meta data.
The branch egonw-ioformats is derived from cdk1.2.x/ and contains the necessary updates:
This patch is ready for review by two senior reviewers, as I like to see it included in the CDK 1.2.0 release.
Attached is a PNG with the new module dependency graph.
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