I've been using GNU stow, and lately xstow to manage package installation on my myriad linux systems:

Today I got fed up. GNU stow is nice, but it depends on perl. xstow is nice, because it can be made into a static binary, but it seems a wee bit bloatish. I can't seem to get either one to support multiple stow directories for a single target directory, so directory splitting doesn't work properly. So, I'm going to write my own: