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SIESTA [Hirshman et al., Phys. Plasmas 18, 062504 (2011)] is a recently developed MHD equilibrium code designed to perform fast and accurate calculations of ideal MHD equilibria for three-dimensional magnetic configurations. Since SIESTA does not assume closed magnetic surfaces, the solution can exhibit magnetic islands and stochastic regions. In its original implementation SIESTA addressed only fixed-boundary problems. That is, the shape of the plasma edge, assumed to be a magnetic surface, was kept fixed as the solution iteratively converges to equilibrium. This condition somewhat restricts the possible applications of SIESTA. In this paper, we discuss an extension that will enable SIESTA to address free-plasma-boundary problems, opening up the possibility of investigating problems in which the plasma boundary is perturbed either externally or internally. As an illustration, SIESTA is applied to a configuration of the W7-X stellarator.