The benefit of an IDE like Eclipse is: it makes working with projects very easy, as generates make files and it takes and automatically manages the make file(s). But sometimes this might not be what I want because I need greater flexibility and control, or I want to use the same make files for my continues integration and automated testing system. In that case a hand crafted make file is the way to go.
One thing does not exclude the other: This article explains how to use make files with Eclipse with similar comfort as the managed build system in Eclipse, but with the unlimited power of make files:
Makefile Project with Eclipse
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