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The Fossil[1] community had this whole process not all that long ago.  Automake/autoconf were rejected as not being portable and being in general a complete pain in the lower torso anatomy to use.  The solution that was used in the end was a little piece of software called autosetup[2].

One of the strengths of autosetup is that it doesn't rely on any tools other than a C compiler and make (at least from my readings of it).  It uses Tcl-based scripts (a strict subset of Tcl), but it includes a Tcl interpreter (in source) that can execute that subset as part of the build process so there's no need for the host environment to supply one.

Given Fossil's goals of being usable, essentially, on any platform that has an ANSI-compliant C compiler (within reason), I think that its adoption of autosetup hints that Lua, with a similar goal, could probably easily do the same.

[1]: http://www.fossil-scm.org
[2]: http://msteveb.github.com/autosetup/