This paper is about generating motion plans for high degree-of-freedom systems that account for collisions along the entire body. A particular class of mathematical programs with complementarity constraints become useful in this regard. Optimization-based planners can tackle confined-space trajectory planning while being cognizant of robot constraints. However, introducing obstacles in this setting transforms the formulation into a non-convex problem (oftentimes with ill-posed bilinear constraints), which is non-trivial in a real-time setting. To this end, we present the FLIQC (Fast LInear Quadratic Complementarity based) motion planner. Our planner employs a novel motion model that captures the entire rigid robot as well as the obstacle geometry and ensures non-penetration between the surfaces due to the imposed constraint. We perform thorough comparative studies with the state-of-the-art, which demonstrate improved performance. Extensive simulation and hardware experiments validate our claim of generating continuous and reactive motion plans at 1 kHz for modern collaborative robots with constant minimal parameters.