We present a black-box method to numerically investigate the linear stability of arbitrary multi-physics problems. While the user just has to enter the system's residual in weak formulation, e.g. by a finite element method, all required discretized matrices are automatically assembled based on just-in-time generated and compiled C codes. Based on this method, entire phase diagrams in the parameter space can be obtained by bifurcation tracking and continuation at low computational costs. Particular focus is put on problems with moving domains, e.g. free surface problems in fluid dynamics, since a moving mesh introduces a plethora of complicated nonlinearities to the system. By symbolic differentiation before the code generation, however, these moving mesh problems are made accessible to bifurcation tracking methods. In a second step, our method is generalized to investigate symmetry-breaking instabilities of axisymmetric stationary solutions by effectively utilizing the symmetry of the base state. Each bifurcation type is validated on the basis of results reported in the literature on versatile fluid dynamics problems, for which we subsequently present novel results as well.