I think you have essentially 3 main choices. (Many other choices as well, but I these are the ones I see the most in the wild)

• Makefiles: I actually prefer these, but it might be because I've used them forever
• CMake: Many open source projects are moving this way and it's got a lot of nice features
• Ant: Normally used for java based deploys but I've been able to use it for C/C++/Perl and PHP as well.

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