The wire protocol is standard libp2p. This is specified here.

The serialization format for blocks is dag-cbor, or raw (unformatted).

Merkle links are encoded as Cids, whose specification is here.

Public signing keys are encoded in cbor, with format specified here.

Public encryption keys are encoded in cbor, with format specified here.

The cryptree+ structure is specified here.

The server API is specified here

The Compressed Hash-Array Mapped Prefix-Tree (CHAMP) structure is specified and implemented here.

The local (service worker based) REST API for applications is described here.