Fortunately, Fossil can now use SHA3-256 as well as SHA-1 (even in the same repository if necessary, perhaps due to upgrading an older repository), and I think it also has a hard mode to detect if SHA-1 collisions seem likely.

(I think git doesn't allow a repository to have multiple kind of hashes; from what I understand, only a single algorithm must be used.)

Since SHA-1 and SHA3-256 have different hash length, you can tell which one it is. It doesn't work so well if the length is the same; one way to fix it would be use a multicodec prefix. (My own implementation (currently incomplete) internally uses the multicodec numbers to identify the hash algorithms, but these multicodec numbers are never stored in the repository; instead, it is only applicable for the argument for the function to compute the hash, which can also be used in other programs.)