Rename --directory to --multiple-files and add --repository command option.

 * config/config.yaml: Add default values for repository items.
 * docs/{cmdargs, config, dbtoyaml, yamltodb}.rst: Document new and
   changed options.
 * pyrseas/cmdargs.py (_repo_path): New helper function.
   (cmd_parser): Add --repository option.  (parse_args): Add helper
   function to refactor common code; store path to metadata under
   'files'.
 * pyrseas/database.py (Database.map_from_dir): Eliminate directory
   argument and and instead use metadata path.  (Database.to_map): Use
   metadata path instead of opts.directory and pass it downstream.
   Ensure we remove old schema directories.
 * pyrseas/dbaugment.py: Rename --directory to --multiple-files (still
   a TODO).
 * pyrseas/dbobject/{__init__, schema}.py ({DbObjectDict, Schema,
   SchemaDict}.to_map): Add metadata_dir argument and use it instead
   of opts.directory.
 * pyrseas/{dbtoyaml, yamltodb}.py: Rename --directory to
   --multiple-files.
 * pyrseas/testutils.py (DatabaseToMapTestCase.to_map): Rename
   directory argument to multiple_files.
   (DbMigrateTestCase.create_yaml): Merge with create_yaml_dir.
   (DbMigrateTestCase.migrate_target): Merge with migrate_target_dir.
   (AugmentToMapTestCase.to_map): Rename directory argument to
   multiple_files.
 * tests/dbobject/test_extern_file.py: Rename directory parameters to
   multiple_files.
 * tests/functional/test_autodoc_dir.py: Instead of saving empty
   metadata files, in the second phase, drop all schemas from source
   database and use that to migrate changes to target.
 * tests/test_config.py: Test repository items.