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I'm talking about some hooks like
- hook_config_info(), that could provide information about configuration files or bundles and be available at boot and also provide which class would handle each config.
- hook_variable_info(), that could provide information about specific variables on each file (name, type, etc) so we can also generate config forms on the fly.
The idea is implemented in variable module, it could be a good starting point, see http://drupal.org/project/variable