The aim of partially and dynamically reconfigurable hardware is to provide an increased flexibility through the load of multiple applications on the same reconfigurable fabric at the same time. However, a configuration bit-stream loaded at runtime should be created offline for each task of the application. Moreover, modern applications use a lot of specialized hardware blocks to perform complex operations, which tends to cancel the "single bit-stream for a single application" paradigm, as the logic content for different locations of the reconfigurable fabric may be different. In this paper we propose a design flow for generating compressed configuration bit-streams abstracted from their final position on the logic fabric. Those configurations will then be decoded and finalized in real-time and at run-time by a dedicated reconfiguration controller to be placed at a given physical location. Our experiments show that densely routed applications gain the most with a compression factor of more than 2× using the finest cluster size, but coarser coding can be implemented to achieve a compression factor up to 10×.