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Quoting myself:
> If someone packages your app for a distribution, they'll
> use whatever method you provide for changing the
> install prefix (generally a PREFIX variable in a Makefile).

Most Makefiles would also use that PREFIX variable to
make a record in the executable of where to find it's
modules. So all a user should need to do for a working
installation is:

  make install PREFIX=/some/custom/prefix

Or a distro packager could use:

  make install PREFIX=/usr

(The Lua Makefile actually doesn't do this, and requires
you to also change LUA_ROOT in luaconf.h.)