Check out draw_common.cpp [2] - the patent work-around is contained in the RB_T_Shadow method:

  // patent-free work around
  if ( !external ) {
    // "preload" the stencil buffer with the number of volumes
    // that get clipped by the near or far clip plane
    qglStencilOp( GL_KEEP, tr.stencilDecr, tr.stencilDecr );
    GL_Cull( CT_FRONT_SIDED );
    RB_DrawShadowElementsWithCounters( tri, numIndexes );
    qglStencilOp( GL_KEEP, tr.stencilIncr, tr.stencilIncr );
    GL_Cull( CT_BACK_SIDED );
    RB_DrawShadowElementsWithCounters( tri, numIndexes );
  }

[2] https://github.com/TTimo/doom3.gpl/blob/master/neo/renderer/...