The objective of this research is to develop a framework for multi-robot coordination and control with emphasis on human-swarm and inter-agent interactions. We focus on two problems: in the first we address how to enable a single human operator to externally influence large teams of robots. By directly imposing density functions on the environment, the user is able to abstract away the size of the swarm and manipulate it as a whole, e.g., to achieve specified geometric configurations, or to maneuver it around. In order to pursue this approach, contributions are made to the problem of coverage of time-varying density functions. In the second problem, we address the characterization of inter-agent interactions and enforcement of desired interaction patterns in a provably safe (i.e., collision free) manner, e.g., for achieving rich motion patterns in a shared space, or for mixing of sensor information. We use elements of the braid group, which allows us to symbolically characterize classes of interaction patterns. We further construct a new specification language that allows us to provide rich, temporally-layered specifications to the multi-robot mixing framework, and present algorithms that significantly reduce the search space of specification-satisfying symbols with exactness guarantees. We also synthesize provably safe controllers that generate and track trajectories to satisfy these symbolic inputs. These controllers allow us to find bounds on the amount of safe interactions that can be achieved in a given bounded domain.