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Mobile free space optical (FSO) links suffer from frequent link blockages due to opaque obstructions or link degradations that can result in degraded or failed networks. In this paper, a dynamic layer-1 based topology and routing control methodology is presented for assuring connectivity in networks with fragile links. Core components of this methodology are described with special emphasis on the dynamic topology optimization algorithm and topology transition schemes. The effectiveness of the proposed methodology depends on the fragility of links compared to the topology optimization duration. If the link fragility is comparable to the time taken to achieve the optimal topology, then this methodology will not lead to a stable network. A companion paper presents link fragility results for various types of terrain and demonstrates that the expected link longevity is significantly greater than the time taken by the proposed dynamic network optimization scheme. Thus, network connectivity can be greatly improved by employing the proposed dynamic topology control methodology and optimization of physical network parameters such as antenna height.