You might be interested in taking a look at SWHID (Software Hash IDentifiers), which defines a way (on its way to become an ISO standard) to reference files and directories with content-based identifiers, like swh:1:dir:d198bc9d7a6bcf6db04f476d29314f157507d505. Yes, it uses Merkle trees for filesystem hierarchy. https://www.swhid.org/specification/v1.1/5.Core_identifiers/
