>>No preference.  It's up to you.  But I'm curious; why are you putting it in an app?

As I do one gnu-build tree, I am going to do its corresponding CMake tree.

The CMake configuration files are generated from Squeak.

It would be like GNU makefiles and autoconf files are generated from Squeak.

Process is like this:

1. have a directory structure.
2. Tell CMakeVMMakerSqueak to generate which creates the CMake infrastructure within the specified directory. (Or generateWithSources to create VMMaker sources and CMake files)
3. from the command line, run the generated buils script 'build.sh' which
      3.a (on pharo, does some git stuff) 
      3.b invokes cmake
      3.c invokes make
4. get your results out of the oscogvm/results directory.

If everything is stable, the end user just does a svn co of the cmake branch they want and invokes the build.sh script. <---THIS is what Tim R. wants as the deliverable

I have another process in place for vm developers similar to your buildsqueaktrunk.sh scripts. I sent you those scripts last week. They set you up with either 
a standard VM build environment (complete with source tree set up relative to Squeak) or a CogVM build environment. The idea being to make it easy on newbie vm guys to get up and running.