No one has mentioned subversion because it is a long way from the OP's needs. isync does no want a version control system that requires the overhead of a server, or will clutter up his file-system with control files and hidden directories.
Most of the posters on this thread, have made the point that both hg and git create only one hidden control directory, have no other administrative overhead, and that the benefits outweigh the trouble.
Subversion while being a fine version control system for many purposes, does fail on both points, In any sensible set-up it requires a server that need set-up and maintenance, and it clutters up every subdirectory of your source tree with .svn directories.
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