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I've just added some instructions for automating the creation of
LuaRocks with GNU autotools-based build systems:

http://luarocks.org/en/Creating_LuaRocks_with_GNU_autotools

I use this method for several projects now, and it saves a lot of time.

autotools fans should also note my ax_lua.m4 helper for Lua:

http://git.savannah.gnu.org/cgit/autoconf-archive.git/tree/m4/ax_lua.m4

For other aspects of using Lua with GNU autotools, real live examples
to study include luaposix: https://github.com/rrthomas/luaposix and
Zile's Lua branch:
http://git.savannah.gnu.org/cgit/zile.git/tree/?h=lua

I'd like to see more integrated support for Lua in the autotools in
future, but to be honest we're only just working out what it should
look like. Nevertheless, anyone who'd like to get involved in
integrating this stuff upstream is welcome to contact me. I'd suggest
that the LuaRocks support would go well in gnulib, while ax_lua.m4
should go into autoconf. automake could probably do with some support
for setting Lua paths for tests & running uninstalled programs.

(Note: I currently can't find time to read lua-l, so only replied
CC-ed to me will actually get read in the near future; sorry!)

-- 
http://rrt.sc3d.org