While experimenting with the latest version of BundleTransformer, I noticed that there is a bug in TransformerBase.cs around line 89. The current version still uses bundleFile.__IncludedVirtualPath__ when it should now be bundleFile.__VirtualFile.VirtualPath__.
This is because Aspnet.Web.Optimizations changed around some things, and without making this change, doing certain things such as a simple "IncludeDirectory(null,null true)" will cause FileNotFound exceptions.
This is because Aspnet.Web.Optimizations changed around some things, and without making this change, doing certain things such as a simple "IncludeDirectory(null,null true)" will cause FileNotFound exceptions.