it´s like this
pixar, or any big company that has a staff of programmers to do what ever they need, make tools they need as they need. but they dont reinvent the wheel.. they use the common stuff like si/xsi/maya for most of it.. but specific things that these apps cant supply as they need, they write plugs..or whole property tools to replace those things. anything from cloth sim,fur.. muscle animation/flexes.. to particle instancing.. what ever they can think of
