Currently options/config for repository plugins is stored in the mdl_config_plugins table with the plugin field populated as just the repo type name.

i.e. for flickr, plugin => flickr, name => somesetting, value => somevalue

This goes against the naming convention and might end up conflicting with mod config settings. Indeed the version setting for each repo is stored as plugin => repository_<name>. Which would imply the settings should be stored as:

for flickr, plugin => repository_flickr, name => somesetting, value => somevalue

As more and more repository plugins are written using this incorrect convention, the chance of a conflicting module of the same name using config increases.
Repository config should be using the full frankenstyle component names.

Upgrading may be tricky in the instance that there are already conflicts out there. A simple replace on the plugin in config_plugins of say s/flickr/repository_flickr/g would be bad if there's an existing module called flickr that happens to use config_plugins for some of its config...