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If I may, I have briefly looked at the autotools and… don't. That thing is a monstrosity. Way too complex.
Wait until your project has 50 files, 10K lines of code, and a dozen external dependencies. Which it won't, because it's a simple VM. I've written a VM for my day job once. It supported a non-trivial number of primitive operations, as well as a high level language (garbage collection, higher-order functions, the works). 2700 lines of C++ code in 7 sources files and 8 header files, zero dependency (besides the standard library). I also needed a compiler, which took 1500 lines of OCaml code.
We used GNU make for the whole project (the VM was but a part of it) and it worked. It was ugly, but sufficient. There's a good chance you don't need more.
implement automake, etc to build the binary.
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