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.vimplugin, 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!