An aside:  Having plugins be  git clone'd means there's no way for them to add gem dependencies.  The very first plugin I'd want to make would thus be impossible (static link checker, it uses the `link-checker` gem).

Alternative idea:  Plugins as gems.  Make a class `Octopress::Plugin` that is a mandatory base class for plugins.  The parent class can receive a method call whenever a sub-class is created, which notifies you of the existence of plugins.  From there, initialization behavior to copy out scaffold/template files can be issued, if need be, by simply having a .plugins.yml file in the user's site root containing a mapping of plugin-gem => version.  If there's no record, no initialization has happened.  If there is a record, and the versions match, nothing needs to be done.  If there's a record and there's a version mismatch, then the user is trying to up/downgrade the plugin.