It's fixed if you reinstalled from the latest update, the plugin is now copied into the "plug-ins" folder of your MAYA_APP_DIR. It doesn't exist by default, but if it's here then Maya will seek for plugins within.
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The null material will be removed from the indigoShader. The layeredShader is for now in charge of managing transparency:
- with one single material connected, the layeredShader will blend it with the null material. The single material must have it's transparency driven by a bakeable node (texture) or oops there's a bug being fixed here. Or nothing
- in the same way than above, when many materials are stacked the last one can be transparent. Tick on the step blend checkbox of the transparency texture for a billboard transparency effect (clip maps).
- I'm reserving the option to use an empty layeredShader to declare the null material.
Have fun
PS: Since I'm not yet into the documentation writing, do not hesitate to ask as many informations as required. In an order please !