rsync. There is a nice side-by-side merge utility: sdiff, but it deals only with two particular files, as well as my favorite choice for this: vimdiff. The closest analogy for this behavior is Gentoo's dispatch-conf, but it's a very specific tool. Well, I've found an elegant solution for this problem, which doesn't require the installation of additional software:
DirDiff.vim plugin, which is using lovely vimdiff feature as an underlying merge. Just put it into your ~/.vim/plugin/ and start with :DirDiff from-dir to-dir.As an example, I've just compared two random directories on my laptop and made a screenshot:
Vim is the power!