I don't want to venture too far off-topic, but when the Perl 6 folks re-designed regexes, they found out that they weren't really designed for anything; the syntax just grew, and common features were sometimes longer than rare ones: http://www.perl6.org/archive/doc/design/apo/A05.html (section "Poor Huffman Coding").

I haven't studied enough of the Git plumbing to know what's going on underneath, but I suspect that the same thing is going on, where features are added without regard to other ones already present (feel free to correct me on this)