You can insert a 'mapFileExtensions="true"' into the deployment manifest (the one with the .application extension) at the <deployment key just before you sign the deployment manifest.
MS Documentation on this key:
http://msdn.microsoft.com/en-us/library/t7050f3w.aspxThis is assuming you are doing a command line change of the deployment manifest and the code signing thereafter via command line.
I did a global search and replace of the key "<deployment " (Note the space) with
"<deployment mapFileExtensions=%%22true%%22 " (note the space and %%22 which adds quotes to the string at command line execution time). Kind of tacky to do that to a XML file, but it works, since the "<deployment " key is unique to the .xml file (and <deployment without a space isn't). If you already have a mapFileExtensions in the key, then this search and replace adds a new one which you don't want.
If you are running command utilities, you can also use XMLStarlet which is a command line utility to process xml file, which was cross compiled from *nix to windows world. That call is rather complicated compared to the search and replace.
If you are running msbuild or nant as a build, then you can find libraries with a XMLPoke or XMLUpdate/XMLMassUpdate task that will do this for you, and I would prefer that to search and replace in a XML file.