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We propose a general and practical planning framework for generating 3-D collision-free motions that take complex robot dynamics into account. The framework consists of two stages that are applied iteratively. In the first stage, a collision-free path is obtained through efficient geometric and kinematic sampling-based motion planning. In the second stage, the path is transformed into dynamically executable robot trajectories by dedicated dynamic motion generators. In the proposed iterative method, those dynamic trajectories are sent back again to the first stage to check for collisions. Depending on the application, temporal or spatial reshaping methods are used to treat detected collisions. Temporal reshaping adjusts the velocity, whereas spatial reshaping deforms the path itself. We demonstrate the effectiveness of the proposed method through examples of a space manipulator with highly nonlinear dynamics and a humanoid robot executing dynamic manipulation and locomotion at the same time.