Someone

eclipse
  plugins
    my.plugin.one
      defines app_one, has help files for app_one
    my.plugin.two
      defines app_two, has help files for app_two
    other plugins
  configuration_one
    config.ini
     (includes org.eclipse.equinox.common@2:start,
               org.eclipse.update.configurator@3:start,
               org.eclipse.core.runtime@start,
               other things,
               my.plugin.one)
  configuration_two
    config.ini
      (the same, but my.plugin.two)
  ...