refactored PDB flags functionality into global state

removed sequential atom list functionality (superseded by atom index)
added atom index (automatically incremented during creation and loading)
coord group uses index sorted atom list instead on relying on the atom order in entity
added coordinate format mae import
added various debug output


git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2056 5a81b35b-ba03-0410-adc8-b2c5c5119f08