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But the identity part of git is not (unless you count pgp signing of each commit, which never took off at a large scale)

and the git tools don't automatically propagate repo changes by default across a network

The identity of a repo is its url so yes, the identity part is decentralized

Identity is more than a name. It is also proving that you own that identity (aka authentication)

Issue tracking and collaboration tools are not. (Although many small projects could get by with a todo.txt and a mailing list.)

But if you just hashed all the changes and put them in Merkle tree to verify, wouldn't that make it so much better?

Yup, but the community you build around a project is not.