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If you are changing any files in this directory, it should be things that should have been in FireBreath to start out with -- things that you might consider contributing back (whether you are actually going to or not is your business). It should not be things that are specific to your project. Things specific to your project should go into your project directory. Most of the classes here that may need to be customized (such as the PluginWindow, NpapiPlugin, or PluginCore classes) can be replaced in your plugin by changing which class you return in your Factory.cpp files in your plugin directory.