Comment by smartmic
I took the trouble (and even spent the money) to get to grips with autotools in a structured and detailed way by buying a book [1] about it and reading as much as possible. Yes, it's not trivial, but autotools are not witchcraft either, but as written elsewhere, a masterpiece of engineering. I have dealt with it without prejudice and since then I have been more of a fan of autotools than a hater. Anyway, I highly recommend the book and yes, after reading it, I think autotools is better than its reputation.