I love Tup, it basically replaced Make for me. It tracks dependencies and files, automatically cleaning and updating everything even more precisely than Make, making it a lot faster and easier to use. https://github.com/gittup/tup

(yes, you can use Tupfiles in each directory, if that's what you mean by packages. As far as I know however, (and this is by design) there is no way to control the build. It will always build exactly what needs to be built to be up to date.)