The BRE Pipeline Framework has now been tested against BizTalk Server 2013 and an installer has been created to ensure the pipeline component gets copied to the correct program files folder. Download the updated installer v1.3.1 from the codeplex project page if you are interested in using the framework with BizTalk 2013. This installer works for BizTalk 2010 or 2013 environments, and allows for the fact that you might have upgraded your BizTalk environment from older versions as well (i.e. your program files folder might still be called BizTalk Server 2009 rather than BizTalk Server 2013 since you went on an upgrade path of 2009 -> 2010 -> 2013).
For a primer on how to use the BRE pipeline framework take a look at this blog post which talks about how it works and how to use it or look at the documentation on the codeplex project page for more information.