Patch fixes two bugs on the CMLReader (actually it's the CMLCoreModule convention). I have implement two tests to demonstrate the bugs and then provided their respective fixes. I'd consider both bugs pretty major (hence priority 8 :D) as you can't really use CML is the given 'flavour' unless you manually modify it.
Atomic number defaulting to 1: https://sourceforge.net/tracker/?func=detail&aid=3553328&group_id=20024&atid=120024
Content of bondStereo ignored: https://sourceforge.net/tracker/?func=detail&aid=3557907&group_id=20024&atid=120024