Personally, I'm more partial to CMake than other build systems for C/C++. Some languages have it better: Python has setuptools or distribute, and Haskell has cabal. These are built with the language in mind and work fine until other things are needed (e.g., asciidoc/xmlto for man pages, doxygen for documentation, and non-standard testing suites (especially when language bindings are concerned and you can't build/use the bound language without hacks)). Others languages still have it hard such as Java with maven or whatever the XML horror du jour is.
What I *really* want is a build system that generates Makefiles (or Ninja files, or Visual Studio projects, or XCode projects, or what have you) (CMake), defaults to out of source builds (CMake and whatever autotools magic glibc has that no one bothers to copy), has a declarative syntax (cabal), and has no need to ship generated files (CMake, raw Makefiles).
I have hacks for CMake to handle LaTeX builds (including double and triple+bibtex passes) with out-of-source builds, symlinking my dotfiles, generating cross-referenced doxygen, and more, but I think a build system that supports something more akin to make's generator rules (something like Prolog/Mercury maybe?) would be nicer to work with (CMake's escaping and argument parsing is less than ideal to manage with complicated things). Implicit know-how of supporting system copies and bundled libraries with automatic switches (which can be disabled if there are patches which make in-the-wild copies not work) would be wonderful as well. CMake's external_project_add gets close, but still has some rough edges (such as needing manual switches for system copies support).
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