In order to realize collaboration on a global scale, academic research requires often large quantities of data to be shared between geographically dispersed organizations. The requirement to protect and govern data in a network of loosely coupled, autonomous institutions is an incentive for decentralized solutions, where the participants are in full control of their data without trusting a third-party provider to store and process the data. In order to increase data availability and fault tolerance in decentralized collaborative systems, we propose a layer, which is based on replication and decentralized authority over the data. The solution consists of an idea of peer-sets, which are groups of peers implementing collective data management, a consensus protocol which synchronizes a distributed ledger between peers, and an atomic commitment protocol used to implement optional two-way references between documents. This architecture may be utilized in various decentralized collaborative data-sharing systems, such as Onedata.