We investigate experimentally the supercurrent in a clean carbon nanotube quantum dot, close to orbital degeneracy, connected to superconducting leads in a regime of strong competition between local electronic correlations and superconducting proximity effect. For an odd occupancy of the dot and intermediate coupling to the reservoir, the Kondo effect can develop in the normal state and screen the local magnetic moment of the dot. This leads to singlet-doublet transitions that strongly affect the Josephson effect in a single-level quantum dot: the sign of the supercurrent changes from positive to negative (0 to $\pi$-junction). In the regime of strongest competition between the Kondo effect and proximity effect, meaning that the Kondo temperature equals the superconducting gap, the magnetic state of the dot undergoes a first order quantum transition induced by the superconducting phase difference across the junction. This is revealed experimentally by anharmonic current-phase relations. In addition, the very specific electronic configuration of clean carbon nanotubes, with two nearly orbitally degenerated states, leads to different physics depending whether only one or both quasi-degenerate upper levels of the dots participate to transport, which is determined by their occupancy and relative widths. When the transport of Cooper pairs takes place through only one of these levels, we find that the phase diagram of the phase-dependent 0-$\pi$ transition is a universal characteristic of a discontinuous level-crossing quantum transition at zero temperature. In the case were two levels participate to transport, the nanotube Josephson current exhibits a continuous 0-$\pi$ transition, independent of the superconducting phase, revealing a different physical mechanism of the transition.