Renaming config and trajectory writer classes.
Removing DDMD_MOLECULES, adding Atom::hasAtomContext flag
Editing param_mcmd.dox
Adding draft of Xml parser classes in util/misc
Merge branch 'devel' of github.com:/dmorse/simpatico into devel
Testing Xml classes in util/misc (they seem to work).
Adding code to clear Xml parsers before matching.