As I see it, you should either check in the flex and bison binaries themselves (and whatever runtime dependences they have) and only use those during the build, or accept that your build will fail and require maintenance as time goes by, doing whatever's simplest without trying hard to avoid that. Autoconf is intended to facilitate dependencies on components outside source control which happen to exist on a single machine, so it's only appropriate to use at all if you go the latter route.