The guys from Cyberduck just use a Cryptomator library for high-level access to some cryptographic primitives, but they still implemented the vault directory layout themselves. We skyped with them to speed up development, but all they need is documented here.
Another example would be a decryption program written in C# by @Larry_E. Larry just used the vault format documentation but no source code from Cryptomator (other than for reference). See this thread for details.