Refactored beastrun_tests and validate_ids

[xrotwang]

• The last failed BEAST XML will be available in ./_test.xml
• Warnings emitted from pycldf are filtered in tests
• validate_ids is called only after writing and saving the XML
• validate_ids detects plate-scope now by looking up parent tags

[xrotwang]

Ah, yes, duplicating was more of an oversight. I'd now unify it, I guess, turning references into a Counter as well, and reducing the code to:

           for attr, collection in [('id', ids), ('idref', references)]:
               if attrib == attr:
                    if e in parent_map and parent_map[e].tag == 'plate':
                        # Quick and dirty plate handling.
                        # We only support plate matching in direct children of the plate.
                        var = parent_map[e].get('var')
                        for id_ in parent_map[e].get('range').split(','):
                            collection.update([value.replace('$({0})'.format(var), id_)])
                    else:
                        collection.update([value])