oBFusCATed, I have done a lot of Autotools reading (from the page you provided, the manuals, and multiple pages search engines have brought up), and begun work on creation of this system. Would it be possible for you (or someone) to post/send me an example configure.ac + makefile.am that could be used to build a small Code::Blocks plugin (like this one)?
I believe having this example of something more complex than the standard "hello world", but still extremely small (only a few files in a single directory) will greatly speed my learning (and give me an example of what a well formatted script should look like). (I have looked through Code::Blocks' Autotools build system, but it is extremely large and interdependent, making it a difficult place to start.)