I've just moved the build files that were formerly in /flashproxy.git/doc to /pluggable-transports/bundle.git. This is a better place because the pluggable transports bundle doesn't really "belong" to flash proxy--rather the opposite.
To build a pluggable transports bundle, follow the instructions in bundle-gnulinux.txt, bundle-macosx.txt, or bundle-windows.txt. In short, once you've set up the environment, you run for example make fetch-gnulinux-i686 make gnulinux-i686 The first command downloads a plain Tor Browser Bundle. The second unpacks the bundle, copies pluggable transports into it, and packs it back up.
David Fifield